I ended up finding a workaround. It turns out the a wildcard union in my FLOW was bogging down the system. I had a couple of inputs that were drawing wildcard unions of excel files with multiple tabs. Most of the tabs were unnecessary. I ended up converting just the data I wanted to union into manageable csv files prior to the prep.
Everything ran has run smoothly after.
Overall, I think the flows get bogged down when a wildcard union has to look through too much data from its sources.