Remember the start of 19/20, for example: after beating Chelsea 4-0 on the opening day, we went eight league games without ever scoring more than one goal in a single game. Or at the end of 18/19: we scored seven goals in the last nine league games. These kind of awful runs do bring down his stats quite a bit.
Even this season: take out the wins against Leeds and Southampton and we have 43 goals in 28 games, 1.535 goals per game which amounts to 53 goals over a whole season. We're not a free-scoring side by any means. Mourinho has a well-deserved reputation for shite football but his teams aren't usually extremely low scorers.