Though Misc. College of Winterhold Tweaks was designed with maximum compatibility in mind, issues may still arise.  Issues arising from conflicts can be solved either by using an offered alternate version of the tweak mod, ensuring that the conflicting mod is loaded after the tweak mod, or simply not using the offending tweak mod.

The Testing Process:  Typically I'll read the mod's description to see what it impacts.  A check in SSEEdit for simple record conflicts is always done first, followed by a peek in the BSA archive, if present, to see if there's any conflicting scripts.  If none are found but information from the mod's description indicates there may still be a conflict (see example below), I check either in the Creation Kit or in-game to ensure that the Tweak still works.  The testing process is not exhaustive (there are many mods to test!) so please do not consider this article to be the last word on the topic.  If you discover contradicting information, please let me know so I can make corrections.

Example:  The Light Pillars fix in ICoW do not seem to conflict with Mage-Light Maintenance, and yet the two mods can't work together due to other changes ICoW makes.

Concerning Facegeoms Bugs:  Misc. College of Winterhold Tweaks makes no edits to any NPC.  All changes related to NPCs are done via quests, scripts, or dialog.  Therefore you should not see an NPC face bug related to these mods.

(XEd) - Tested in SSEEdit
(CK) - Tested in Creation Kit
(IG) - Tested in-game
(SC) - Conflict is in Scripts

Alternate Start - Live Another Life
   ▪  Mage-light Maintenance - Load MLM after AS-LAL.

Apepi's Better College of Winterhold (XEd)
   ▪  Erratum Etc. - Incompatible:  Use EEtc. Lite.

Better College Application (XEd) (IG)
   ▪  No conflicts found

Better College Students Room (XEd)
   ▪  No conflicts found

Book Covers Skyrim (XEd) (IG)
   ▪  No conflicts found

College Days (XEd)
   ▪  No conflicts found

College Grounds (XEd)
   ▪  No conflicts found

College of Winterhold Light Pillar Fix (XEd)
   ▪  Mage-light Maintenance - Redundant:  Fixes the light pillars by another method.

College of Winterhold Upgraded (XEd)
   ▪  Erratum Etc. - Incompatible:  Use EEtc. Lite.

College Modifications (XEd)
   ▪  Scheduled Savos  - Minor Conflict: Both mods add a key to Savos' inventory.  No load order fix.

Cutting Room Floor (XEd) (IG)
   ▪  No conflicts found

Enlightened College of Winterhold (XEd)
   ▪  Mage-light Maintenance - Redundant:  Fixes the light pillars by another method.

Faction Skill Requirements (SC)
   ▪  Dead Dunmer Delivery - Incompatible:  Both mods edit the same quest script.

Finding Velehk Sain (XEd) (IG)
   ▪  No conflicts found

Guards of Skyrim - College Guards (XEd)
   ▪  No conflicts found

Immersive College of Winterhold (XEd) (CK) (IG)
   ▪  Mage-light Maintenance - Redundant:  Fixes the light pillars by another method.
   ▪  Governable Gatekeeper - Minor Conflict:  ICoW disables the trigger GG uses.  Load GG after ICoW.
   ▪  A Wizard's Walk - Redundant:  Already contains A Wizard's Walk.
   ▪  Scheduled Savos - Minor Conflict:  Both mods edit Savos' courtyard AI Package.  Load ICoW after SS.
   ▪  Erratum Etc. - Incompatible:  Use EEtc. Lite.

Immersive College NPCs (XEd) (IG)
   ▪  No conflicts found

Improved College Entry (XEd) (IG)
   ▪  The Augur’s Admonishment - Redundant:  ICE includes a modified version.
   ▪  Mage-light Maintenance - Redundant:  ICE includes a modified version.
   ▪  Scheduled Savos - Possible Minor Conflict:  Both mods add a key to Savos' inventory, but I was unable to find a case where he had two keys.  No load order fix.
   ▪  Friendly Faralda - Redundant:  Included in ICE.
   ▪  Erratum Etc. - Semi-Redundant:  ICE includes all fixes from EE except locking the Arcanaeum bookcases.

Juniper's College of Winterhold (XEd)
   ▪  Erratum Etc. - Minor Conflict:  Load JCW after EEtc.

Mage College Dorm Doors (XEd)
   ▪  No conflicts found

Magical College of Winterhold (XEd)
   ▪  Erratum Etc. - Incompatible:  Use EEtc. Lite.

The Midden - Expanded Lite (XEd)
   ▪  No conflicts found

The Missing Apprentices Quest Fix (XEd) (IG)
   ▪  No conflicts found

More Tavern Idles (XEd) 
   ▪  Friendly Faralda -  Minor Conflict: Tavern Idles edits Faralda's package to make her not always be at the foot of the bridge.  I recommend loading FF after it to overwrite TI's changes.

Nether Mage Armor (XEd)
   ▪  No conflicts found

Not So Fast - Mages Guild (XEd) (CK) (IG)
   ▪  The Augur’s Admonishment - Update Available:  Version 1.0.1 of Misc. CWT contains a version of TAA which works with NSF-MG.

Obscure's College of Winterhold (XEd) (CK) (IG)
   ▪  The Augur’s Admonishment - Update Available:  Version 1.3.10 of OCW and newer is fully compatible.
   ▪  A College Coup - Update Available:  Version 1.4.03 of OCW and newer is fully compatible.
   ▪  Arniel's Appeals - Update Available:  Version 1.4.03 of OCW and newer is fully compatible.
   ▪  Scheduled Savos - Redundant:  All changes have been copied into OCW (as of version 1.3.10)
   ▪  Erratum Etc. - Redundant:  All changes have been copied from OCW.

Okata's College of Winterhold - Thriving Edition (XEd)
   ▪  No conflicts found

Opulent Outfits (XEd)
   ▪  No conflicts found

Toberone's Winterhold College (XEd)
   ▪  No conflicts found

Winterhold Bridge Fix (XEd)
   ▪  No conflicts found

Winterhold College Hideout (XEd)
   ▪  No conflicts found