An incorrect external link won't prevent any pages from being indexed. Typically, these are links where the domain name is correct, but either the filename is wrong, or it's got some spurious characters tagged on the end. Google will report these in Webmaster Tools, but they won't do you any harm.
Wondering if G is changing the way they are reporting 404's
No, not that I've heard of. I'd be very surprised if they had.
Also, I thought there might some sort of penalty for overuse of the 301
Again, no. I've never heard of this, and it would be surprising if they did do any harm.
If you're sure you haven't intentionally blocked any pages (on many sites, things like contact pages or privacy policies are intentionally blocked), your only option is to try to figure out which pages aren't indexed, which will be laborious and time-consuming. Alternatively, you can just not worry about it. You say you've got 228 out of 230 pages indexed. Chances are that's enough to bring you the traffic you want.