Issue #1: The old structures are overlapping the repaired structures or stuff (like trash) is still there that shouldn't be.
Information: This is 100% a load order issue or a conflict with another mod that makes changes to the same area. Read the FAQs and the Previsibines and PRP article for more information on figuring out your load order. Example:
Solution: The Rebuild_SettlementName_Previs.esp file MUST BE AT THE BOTTOM OF YOUR LOAD ORDER. The order of the previs files if you use multiple standalones does not matter EXCEPT for Sanctuary, Starlight and Red Rocket. The order is Red Rocket, Sanctuary and then Starlight last.
Issue #2: Things are blinking in and out of existence.
Information: Same as issue #1. This is a load order issue or a conflict with another mod that makes changes to the same area. Try just the Rebuild mod, Previs esp and Shared Resources by themselves. If you still have issues, then let me know (with a screenshot). 90% of the time it is a load order issue but occasionally it could be that a mesh is overlapping a cell border and I need to redo the previs patch.
Solution: The Rebuild_SettlementName_Previs.esp file MUST BE AT THE BOTTOM OF YOUR LOAD ORDER. The order of the previs files if you use multiple standalones does not matter EXCEPT for Sanctuary, Starlight and Red Rocket. The order is Red Rocket, Sanctuary and then Starlight last.
Issue #3: Everything is all stretched out.
Like this (thanks to Mora for the screenshot): 
Information: Same as issues #1 & #2. This is a load order issue or a conflict with another mod that makes changes to the same area. Try just the Rebuild mod, Previs esp and Shared Resources by themselves. If you still have issues, then let me know (with a screenshot). 90% of the time it is a load order issue but occasionally it could be that a mesh is overlapping a cell border and I need to redo the previs patch.
Solution: The Rebuild_SettlementName_Previs.esp file MUST BE AT THE BOTTOM OF YOUR LOAD ORDER. The order of the previs files if you use multiple standalones does not matter EXCEPT for Sanctuary, Starlight and Red Rocket. The order is Red Rocket, Sanctuary and then Starlight last.
Are we sensing a theme here?
Rebuild_Settlement_Previs.esp plugins need to be below all other mods!
Issue #4: I've highlighted the items in workshop mode but there is no option to repair.
Information: You installed the mod when the cells were loaded. For example, if you are in Sanctuary, save and exit the game and then install Rebuild Sanctuary this will happen because the script won't run on areas that are currently loaded.
Solution: If you've already installed the mod, just fast travel FAR AWAY and back again. It has to be far enough that the cells are unloaded.
Issue #5: I can't find the item to highlight in workshop mode in order to do the repair.
Information: I've tried to use items that blend it so some may be somewhat of a hunt to find. If they are actually missing, then you don't have the plugin loaded.
Solution #1:The list below gives an overview of the items used for repairing structures. If you still can't find them, follow the link to the settlement's standalone version and look at the screenshots.
Castle - Use the piles of brick and cinder blocks next to the walls to repair. There are 2.
Coastal Cottage - Use the plywood doors.
County Crossing - Use the plywood leaning up against the ruined house to repair
Covenant - Highlight the house, bay window and porch.
Croup Manor - Repair each individual wall, floor, roof, etc
Egret Tours Marina- Use the plywood doors, pallet, barrels, construction barrier.
Graygarden - Individual wall pieces on the greenhouse.
Greentop Nursery - Highlight the House and individual wall pieces on the greenhouse.
Jamaica Plain - There is plywood over the doors of the boarded-up houses. Open houses have plywood next to the doors. City hall - use the mannequin. Diner - Use the sign.
Kingsport Lighthouse - Wall of the house and pier house. Highlight the lighthouse to clean it.
Murkwater - Barrels by the house and shed.
Nordhagen Beach - The walls with windows.
Oberland Station - Use the plywood over the door.
Red Rocket - Use the tire to the left of the garage door opening.
Sanctuary - Use the construction barriers in the houses. Ruined houses, highlight the house. Roads are repaired using the construction barrier in the garage next to the diagnostic cart.
Slog - Walls with windows. Unlock the diner door to repair it.
Somerville Place - Plywood next to the workshop.
Spectacle Island - Walls of the house, greenhouse/shed and pier house.
Starlight Drive-In - The plywood door over the Diner door, and the plywood door leaning up against the shed.
Sunshine Tidings - Plywood doors for each cabin.
Taffington Boathouse - Repair each individual wall, floor, roof, etc.
Tenpines Bluff - Highlight the house.
Warwick Homestead - Metal barrels by the catwalks.
Far Harbor:
Dalton Farm - The ruined house and shop.
Echo Lake Lumber - It's a treasure hunt. See screenshots on the mod page if you can't find the repair items.
Longfellow's Cabin - Barrels next to the cabin and shed.
National Park Visitor's Center - It's a treasure hunt. See screenshots on the mod page if you can't find the repair items.
Nuka-World:
Nuka-World Red Rocket - The tire to the left of the garage door.
Solution #2: If they are completely missing, you don't have it installed correctly. If you are using Vortex, then go to the Plugins tab and make sure the plugin is enabled.
Issue #6: Items aren't blinking in and out of existence, but are simply not there at all.
Information: When I update the mods or add a new one, I sometimes need to add new items to Shared Resources. If you haven't updated then it won't find the meshes for the new items.
Solution: Update to the latest version of The Rebuild Collection - Shared Resources.
Issue #7: I get a CTD when starting the game.
Information: When I update the mods or add a new one, I sometimes need to add new items to Shared Resources. If you haven't updated then the game can't find the item and can cause the game to crash. Another possible issue is that you have Shared Resources loading after the Rebuild mod but since Shared Resources is a master, this really shouldn't happen unless you are manually installing mods.
Solution: Update to the latest version of The Rebuild Collection - Shared Resources and make sure it is loaded before any of the Rebuild mods.
Issue #8: I'm getting pink/purple textures on the doors in Sanctuary and/or the doors in Rebuild - Workshop.
Information: Pink/purple textures means that the game cannot find the texture files. This is an issue with AMD graphics cards. Thanks to ShadowPandah for helping me figure out the issue and testing.
Solution: Download the AMD Door Texture Hotfix from the Update files. As of v2.1 of The Rebuild Collection - Shared Resources, this has been integrated into the main file so just update if you still have this issue.
Issue #9: When repairing a structure, the UI says I need 60 steel (for example), but only 6 steel are removed.
Information: This is a "feature" of the vanilla repair system. It checks number of settlers, defense and other factors for the settlement to determine how much of the item(s) needed for repair is/are actually taken.
Solution: There is no solution. It's a vanilla thing and there is nothing I can do about it as is. I was going to work on a script that bypasses the vanilla script's calculation for determining how many resources are taken, but the Next Gen update put that on hold.
Troubleshooting
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Bunker Hill - Highlight the tall junk wall that covers the doorway on the right of the main building.