I have a project which is to design an IC tester, long story short, I and my team members made the design and "theoretically" it should work just fine, but for some stupid reason, a 2 bit counter counts like this (0>1>2>0>2>3) instead of (0>1>2>3) but keep in mind I've tried testing it separately and it works, but I can't wrap my head around why it won't work while being inside my circuit. I use logisim for simulation, you can see that "Counter 2" and "Case Counter" connected to the same enable function, and yet "Case Counter" works properly but "Counter 2" doesn't.

 

Ah, yes, those unidentified IC blocks and unnamed signals really make things clear to an outside reader.

 

Welcome to AAC!

you can see that "Counter 2" and "Case Counter" connected to the same enable function, and yet "Case Counter" works properly but "Counter 2" doesn't.

We can't see anything. You have a blocks labeled "Case Counter" and "Counter 2", but we don't know what's in the blocks.

What do "AllGatesEqual", "Register", "Compare Circuit", "Result Modifier", and the block under "IC Under Testing" do?

You should learn how to draw neater schematics. That will make it easier for you, and others, to read them.