That is likely one of them. Ironically, "The Child", despite it being pretty much a bottle episode, is likely another. Ten-Forward debuted here, and that was a permanent set. As such, it's cost is much higher to build than a swing set, such as one with alien planets. Plus, Whoopi Goldberg. She may not have asked for a lot of money due to being a fan, but she certainly couldn't have been cheap, particularly since she won a Golden Globe and was nominated for an Oscar by that point in time. She was in at least 5 episodes that season.
I am pretty sure the bridge was moved from one stage to a larger one, so that likely added cost.
If memory serves me, budgets for episodes could be carried over to later ones, allowing a bit of breathing room. But that also backfired, as it probably meant being overbudget for several in a row without really realizing one last one was still needed to be made.
And yes, in a sense you were right... time, after all, is money. And a lot of valuable production time was lost at the beginning of the season.