Gonna try to keep a list of the pending fixes of stuff that people report. If you can report stuff on this thread too, just to make it easier to keep track of. Before reporting check the known issues in the main description and here.

If you are crashing on repentance, check the log before relaunching the game, on the last few lines it will tell you the lua file that crashed and which mod was responsible. If its a lua thats on da rules folders then copypaste those last lines here, I wanna see them.
(your log.txt file is located in "Documents/My Games/Binding of Isaac Repentance" for repentance)

Now, after that (or if you are not on repentance), please tell me what rules you currently have active or if they are too many to list (or if you are kind enough), give me your modded save file so I can check them myself.
(Modded save on AB+: Documents/My Games/TBOI AB+ Mods/Da Rules_XXX/SaveX.dat)
(Modded save on Repentance: Main Game folder/data/Da Rules/SaveX.dat)

- I cannot open the menu or the menu appears empty and I cannot create rules:
This usually means corrupted rules, so you either ♥♥♥♥♥♥ up while creating a rule(maybe using a nonexistent entity) or a bug happened while creating a rule and it got messed up. You can solve this by doing the command "clearrules" (to delete all rules on the current set) or "deleterule X" if you remember which rule was it that ♥♥♥♥♥♥ up.
Even if you do solve it this way, still, let me know of what happened so I can fix potential issues!
Alternatively, you can clear your rules from the modconfigmenu.

- I got locked out of the game due to a rule
Enter the "disable rules" custom challenge and then remove the problematic rule....or use either the "clearrules" console command or the "deleterule X" console command if you remember the rule that got ♥♥♥♥♥♥. You may need to start a new run too, depending on what you did. Then start a new run and reenable the rules by clicking the "Rules" text on the bottom right of the menu.
Alternatively, you can clear your rules from the modconfigmenu.

-"I ♥♥♥♥♥♥ up the open key and now I cannot open the menu!!"
open the onsole and do "openkeyrules j" or, if you have modconfigmenu, just go to the Da Rules section and set the Open key or force open the menu.

- Using a controller as P1, will spam babies when you press enter. The input cancelling abilities of the api exclude the joinmultiplayer action...so theres no way to fix this one sadly. You can use Right shift and right CTRL instead of enter, to confirm inputs and prevent this issue. (reported by Danizk0)

- Familiars spawned using the rules(or the debug console) are not permanent, this is a game issue, theres not much to do there....if you want permanent familiars, give Isaac the corresponding item instead, using the "give item" special. Some mods are also known to instantly remove familiars when the player doesnt have the item, so take this in mind too.

- Open the menu in greed mode clears waves and the stage rules dont work there (I dunno what greed mode is tho)

- Use active item doesnt work for Esau Jr and spin to win: this is due to those items being coded like absolute ♥♥♥♥ and theres not much I can do about it.

- Some conditionals wont work on item pickup since the item cease existing on pickup (API ISSUE)

- Co-op is not fully supported so some stuff wont work properly while playing co-op, like stats modifications, for instance.

-Waiting for reports

- Coloring GridEntities and overall oddities with sprites on gents (api bug)
- Stats are odd (rep changed how they work and they get wonky the higher you go)