I didn’t play for a few weeks, but since the latest Update (for me it was the latest) this also happens to me.
I would say 2-3% of my mousclicks doesn’t show any effect - did the devs introduce a new way of receiving mouse clicks? It feels like there is a bug there which happens. Or a timing issue where mouseclicks are missed. Or the queue in which villagers actions get saved have a bug. Related. Thank you!