If the OP hasn’t done so already, pick up A Man on the Moon, by Andrew Chaikin. It goes into a lot of this stuff.
Off the top of my head…
Apollo 11:
Armstrong switching to “manual” during the landing wasn’t exactly a glitch. Theoretically, the LM could reach the surface without any intervention (except possibly shutting down the engine, I’m not certain…). But the astronauts generally planned to take over control at some point prior to touchdown. And I have “manual” in quotes because there were a number of levels of automation. I’m not sure any of them were completely manual in the sense that the astronaut was making raw data control inputs. You could say he was flying by hand, but as I understand the LM’s systems, he could also be said to be sharing control to some degree.
Anyway, Armstrong took control sooner, and for longer, than had been anticipated.
Also on 11, they had to use a pen cap to push in a breaker prior to liftoff from the lunar surface. The switch itself had been broken off at some point. Even without that fix, they would have had several ways to fire the ascent engine.
12:
Already covered. But what I find most interesting is that NASA worried the lightning strike might have damaged the pyrotechnics that deployed the parachutes. They decided they may as well fly the mission and see what happened, a decision that would probably not go the same way today.
13:
Already covered. But I’ll add that despite the drama in the movie, there was no tough decision to close the reaction valves, thereby negating the possibility of landing. When the explosion happened those valves shut automatically, and the mission rules were clear that the landing was off. Lovell knew that, and if you listen to the actual audio you can hear the disappointment in his voice. The famous “Houston, we have a problem” is wrong. It was, “…we’ve HAD a problem”.
14:
Before the drama with the landing radar, they couldn’t dock the two spacecraft. Very nearly aborted the whole landing early on. Then on the surface, Shepherd and Mitchell lost their bearings and couldn’t find the crater they were looking for.
15:
A vice on the outside of the LM was installed backwards, so they had trouble disassembling the core samples they’d worked hard to obtain.
16:
They had problems with the command / service module backup control systems. Ken Mattingly was worried they’d cancel the whole thing and that he’d screwed it up.
17:
There was a change of ground receiving station / frequency just at the moment of liftoff from the lunar surface. Nobody realized that, so once they had blasted off they found themselves with no comm. Astronaut Jack Schmitt changed antennas or frequencies or something and reestablished communications. I got to talk with him about that once when I was interviewing him for an article I wrote.