It appears to be a bug-- certainly, the "missing" angle parameters are nonsensical, as HA (aliphatic H) is the wrong H atom type for NH3+ (it is HC in the PRES definition for NTER). Also, an H atom shouldn't be the central atom of an angle term, either.
It only seems to break like this for a single amino acid, however; it fails for just Ala, but works fine for Ala-Ala.
Analysis of the NTER and CT3 definitions in the residue topology file (RTF) indicates a probable cause-- the H atoms on both the NH3+ of NTER and the CH3 of CT3 have the same atom names, so there are duplicate HT1, HT2, and HT3 atoms in the same residue as a consequence of the double patch. This is a violation of the RTF rules, and is consistent with most of the "missing parameter" messages as well.
Either use longer peptides (2 or more AA), or else edit one of the PRES definitions to change the H atom names so that they do not conflict.