I get a lot of confusing yellow highlighting when using HoTT-Agda, which I initially ascribed to inability on my part, but have now reduced to a simple example which has left me just as confused, yet not so assured of my guilt:
https://gist.github.com/aerskine/7962608
When I load this file with Agda 2.3.2.1 the S m == S n term is highlighted yellow, with missing metadata as indicated in the comments.
However, upon commenting out the import statements and replacing with the cut / pasted code from HoTT-Agda the problem vanishes.