Jacob Blevins - without seeing the assembly and or your feature tree, the answers to your question could be wrong or vague at the least.
The most important portion of designing with Solidworks is here.. The Design Intent Thread Depending on the Design Intent and the assembly layout the nest thing that comes to play is Skeleton Sketch Part Method for Large Assemblies
To take a stab at your issues, the first thing I would say... It's possible you have Circular Rebuild Issues or parts designed in context within the assembly and there are related parts missing or changed etc..