1. It has an internal edit system that is more often than not incorrect. And there is no way to turn it off, apparently, or correct it. You can bypass it by not scrubbing your claims, but still...if you do scrub,it should work right. It will tell you codes need modifiers when they don't, that dx's aren't covered when they are, etc.
2. It considers each line of service for a DOS to be a separate "claim". This can be a hassle when you need to fix something with a claim, or make a note on a claim, etc.
3. Entering or deleting dx's for claim lines can be tedious. I use a lot of procedure macros because of this.