I had an overheating issue that plagued me for a few months when I first got the boat. I needed a haulout for that one, as the problem was a broken check valve in the lower unit. That put me down one engine.
I had a coupler strip out, which was another haulout repair. Down one engine.
I had a fuel filter pack up on me, which knocked one engine out. I thought I had a spare, but didn't. Turns out replacements are extremely hard to find. The same trip I had a fuel pump die on me. Down one engine.
I had lots of problems with my shift/throttle cables not wanting to stay properly adjusted for any amount of time, causing either/both engines to stall out at inopportune times.