Although there are non-canonical amino acids (beyond the canonical 20) in natural proteins.
I also don’t think that most ncAAs stop the protein being a substrate for the proteases in your gut so you can still break it down to its constituent amino acids (then excrete any that you can’t reuse or break down further).
Finally, you eat plenty of large indigestible molecules, like cellulose, with no ill effects.
The only real problem would be if the ncAA (or the protein) was actually toxic.
