I haven't had the chance to watch Saturday's game yet so can't comment on that but it's not just a personnel thing that causes it's a variety of things.
Goalkeeper - Either Alan Martin is rooted to where he is because he can't physically move or Leighfield is too short to come for a cross. The inconsistency probably doesn't help as i'd imagine they'd rather have Martin as they'll naturally have more faith in him as first choice compared to Leighfield.
Defence - How often does the defence end up camped in their box late on and don't push up? I don't know if it's a fitness thing (Likely seeing as they are low level full time players in a small squad), or just laziness but you have to play with some intensity to do your job which is probably more annoying. Also just basic marking at times is deeply frustrating, Darren Brownlie has played a lot of football at a young age so frankly he should be able to communicate better rather than being the common denominator in the decline of a solid defence over the last 3 years. but you can say the same of almost all of the defence. Fortunately Shaun Rooney is gone so we'll concede a million less fouls from hands on back now, (Thank god the SPFL is too skint for VAR).
Crosses coming in, firstly playing strikers out wide and expecting them to track back is asking for trouble, almost all of Dyke's bad performances came when he was on the wing, but as has been mentioned Stirling doesn't like to do it, neither did Dom Thomas. The only one i thought that did a good job of it was Murray but he is pretty limited at the whole going forwards thing. Mercer isn't particularly mobile or great going forward though so when he had bad days, it was a bloody mess. When you added in John Rankin being so far behind the play that he was in a Dundee United shirt there wasn't much protection for the full backs.
Size matters - As mentioned Leighfield is rather short for a keeper, Marshall, and Mercer aren't big, Brownlie and Fordyce aren't huge centre halves, there wasn't a particularly strong dominant midfielder either. As mental as it sounds, big people tend to be better in the air (Not a guarantee see, Cameron, Kyle).