is there any way to fix the alignment of rythmic cues?
It’s aligning on the left edge of the note head, rather than the stem.
No, and I think this is actually the correct alignment, since the rhythmic position is at the left-hand side of the notehead. It would be different if they were on the same stem as the full-sized notes, of course, but this is “correct” in terms of where the simultaneity exists.