I have a tiny yearling. He was a year the end of may 12.3 at the wither and 13.2 at the hip. Mom is 15.1 and dad is 15.2-3. 

Anyways, he has hit a plateau and hasn't grown at all the past few months. He looks really pretty and put together, gets good nutrition. He just isn't growing. I'm worried I'll have a 13 hand pony.  Has anyone else had this?

I've had several who were punky as yearling/long yearlings and all but one grew into normal 15hh+ horses. One was by a 14.1 stallion and 14.2 mare and she stayed small at 14hh, but was balanced and built. One was punky as a long yearling but sprouted in the following 6 months to almost 16hh - took her another year to get those legs under her but she is now a fine 4yo getting on the pattern. 

They tend to go through growth spurts in the spring and fall, a lot don't grow much between those phases. My last colt was 12.1 as a yearling and 13.1 as a 2 year old, he ended up being 15.2 by the time he was 4. I have another mare that just grew an inch this spring as an 8 year old. Your colt will grow fine, I wouldn't worry about it