Welcome to the forum. It's going to be difficult to diagnose the problem without having the model. If you want to post the assembly someone can take a look. Click on "Use advanced editor" at top right to post parts. Be sure to include the assembly and parts. The easiest way is to Pack and Go the assembly to a zip file.
As an alternative, you might want to just place circles in your assembly sketch coradial with the holes in the part (or sketch points concentric if you're using the Hole Wizard) instead of using convert entities.