Several possible reasons for this (in order of importance):
1. An extremely unbalanced lineup. The stars at the top of the lineup are constantly getting on base and creating 'clutch' situations that the mediocre to bad players at the bottom can't take advantage of.
2. Lots of similarity in the lineup. Aside from Altuve, most of the Astros' hitters are 'three true outcome' types (some are just better at it than others). They have the same basic strengths and weaknesses and will all perform well or poorly in certain circumstances (opposing pitcher, pitch selection, ballpark and conditions, etc.). This leads to a boom and bust cycle where they're almost always either blowing out the other team and 'wasting' lots of runs or struggling to score at all. When the pitching staff is doing well, as it did for most of last year and part of this year, the latter situation leads to close and low-scoring games with lots of 'close and late' situations that the Astros have little chance of converting to runs and wins.
3. Lots of young players who don't (yet) perform well under pressure.
