It sounds like you might be using WolframAlpha to try to do your integrals. That has a relatively short line length limit and when you exceed that it seems that it truncates the rest of the line or confuses the recognition system. If that is what is happening then that would explain what you are seeing.
If you could edit your post to include a few typical example integrals and either indent each of those or use the double quote button at the top of the posting window to accomplish the same thing then that would keep the posting process from interpreting some characters as formatting instructions instead of raw mathematics.
With those readers would hopefully be able to reproduce the difficulties you are seeing and possibly suggest ways around this.
If you are dealing with simple polynomials then you might see if you could split one integral into several, integrate each independently, extract each result and then add the results as a later step.