You seem to be confusing "operations" with "mechanical operations." When I say "Ops," I mean it in the Disney sense—loosely defined as daily operations within the parks. This covers crowd control, attraction throughout, etc.
Here's one example. By creating artificially long lines at large capacity attractions, FP+ has affected Ops by decreasing hourly throughput in some of the locations. Consider that POTC has two loading decks, but if few guests are picking up FPs, everyone is backed up on one side even though every other boat is empty. Sometimes the attraction CMs can help by splitting the standby queue and sending guests to the FP side, but that's only if scheduling allows the position.
POTC is then operating below its capacity, making queues longer and crowds more difficult to manage. It also leads to decreased guest satisfaction.
Remember, FP+ was added to those attractions because it was originally a shell game. Someone sold execs on the idea that by moving guests around from pre-scheduled queue to pre-scheduled queue, the company wouldn't have to invest in new attractions to absorb crowds. It seemed like a win-win situation: eventually, guests would schedule their entire days in advance and Disney wouldn't have to build multiple expensive attractions. It was an incredibly shortsighted and arrogant plan that also assumed guests were addicted to Disney and wouldn't care that the parks were becoming stale. Then Potter happened.
Back during the days of FP+ testing, front-line Ops CMs repeatedly complained that the system wasn't working. After Disney added FP+ to the omnimovers and boat rides anyway, front-line CMs were proven correct, and the system has had to be tweaked repeatedly to fix a problem that didn't exist before a substantial and unneeded investment.