I had a similar problem, but eventually figured out what I was missing.
For the former case, I assume either the 3s or the 9s was the riichi tile. Generally speaking, suji information from the riichi tile is considered less valuable; for the purposes of this trainer, the riichi tile should be ignored when determining suji by the standard "three away" method.
For the latter case, there was probably a wall on 2m or 3m. If you can see all four 2m or all four 3m, the attacking player is obviously not holding 23m; so 1m can be considered suji.