It could be that there was a setup change before Sprint qualy as @SSJ4 says. Maybe Aston lowered downforce but that made the car uneasy to drive? However I think they should have gone through to SQ3 regardless.
I can see at least 4 mistakes around the SQ2 lap. Turn 1, Turn 13, Turn 15 and Turn 19. Ill use Magnussens lap as comparison. First turn 1
Even after missing the apex and losing what looks like a tenth and a half from that, the rest of sector 1 and 2 is decent and arrives at the end of sector 2 completely equal to Mag. But here comes the Turn 13 & Turn 15 mistakes
Which makes him lose two tenths and a half compared to Mag. Lost the rear in 13 and missed the apex in 15. Finally he went long in the penultimate turn and lifted trying to avoid track limits although it got cancelled anyway, and the last one didn't seem to be good either. Another two tenths lost which puts him 4.5 tenths behind Mag.
It could be that the car might have been more difficult to drive after the setup change, but in any case to me it seems that both Alo & Stroll were poor and a better driver could've put the Aston in SQ3. Imo with a clean lap before sector 3 it could have been a tenth quicker than Mag and finish the lap a tenth behind or so overall, but not 4.5 tenths. Alonso continues to show signs of aging in my view but Stroll is hiding them somewhat.