Without knowing anything specific about the structure of your comp(s) and the expressions involved nobody can say anything. Typical candidates for such failures are the absence of layer space transforms or enabling continuous rasterization... Eitehr way, you would have to provide screenshots and all that or even the project itself...
As Mylenium said there are just too many variables in your question to come up with any suggestion other than making sure that your expressions tie one comp to another. For example a Effect Control position slider in the MainComp can be tied to a layer in SubComp by referencing the MainComp in the expression added to the SubComp.
You can build a series of expressions that replicate parenting behavior. Those expressions would work across comps, but you cannot simply parent a layer in one comp to a layer in another. These expressions could as easily point to transform properties of the null layer. What makes them work is the value + operator.
A positioning expression that replicates the parenting behavior and allows key framing of both layers without having to re-position the child layer to correct alignment looks like this:
ipw = comp("Comp 1").width/2;
iph = comp("Comp 1"). height/2;
ip = comp("Comp 1").layer("Null 1 controller").transform.position - [ipw, iph];
np = value + ip
Sorry about that everyone. I really appreciate you responding though!
I have attached three different character compositions to help in understanding the problem.
The effect seems almost random. It will work for a bit with one character and then not work at all anymore once all of the characters are in the same composition.
Unfortunately I do not have the original file where it was breaking since that is at my work computer at the studio. I hope this is enough!