And it's just one of those things you learn to live with? Or is it something I don't understand?

Specifically Motion 3 (FCS2).

I'm not that familiar with it, but I'm getting to know it, and there are some things that just behave strangely (or so it seems) and I have no idea why.

For instance -

Messing with a bezier curve I created, altering the points. The bezier handles start out where tweaking one "arm" makes the other one move in tandem. Then sometimes, they just stop doing that and each arm can be moved individually without affecting its opposite. No idea why.

Trying to use keyframes to animate this same curve, actually animating the bezier points. Works as intended, but if I try to MOVE the keyframes to change the timing, seems like it's ignoring it. Keys act as before even when moved.

-Sometimes, I swear keyframes just don't show up in the keyframe editor. The colored lines for different animated parameters will appear, but the actual key nodes themselves will not

-text will "freak out" sometimes on playback. Like if I have a single line of text, it will suddenly become two lines, with several letters forced onto a second line, but just for a moment.

Is this just part of the "charm" of the program or do all these things have real causes?

the weird text thing may be a graphics card issue, as Motion relies heavily on the card. do you use two displays? that can cause weirdness.
as for the beziers, using the option/control key changes if the nodes act in tandem or separately. also, if you control click a node, or drag a highlight over a bunch of nodes, you can control click to change how the curves fuction: ie. as linear or bezier or ease in etc. and there is a drop down menu to choose which key fame parameters are displayed, and choosing 'animated' will show only those altered. if the nodes aren't showing on animated parameters, then i have no clue why that should be...
using behaviors to animate can be easier than doing it manually with key frames, and you can always alter the key frames of behaviors to get more control.
when i first started using Motion 3, it made me cry. often! after a few years i really love how powerful this program is. but yes it is really quirky. it still will freeze up if you throw too much at it or perform very slowly, but if you walk on egg shells and work smartly (and save often), it is amazing what can be achieved! also, i think live type can be a problem in the program and i avoid it...

Good call on the bezier node "arms". I'll look into it.

I do NOT use two displays, but I am on an '08 Imac.

-here's a new wrinkle. . .if you have text, and add a "grow" behavior, and use extrude, it will jitter around unpleasantly as it grows. Take extrude away? Now it's fine. Why? Who knows.

Yes, doing most tasks, as evidenced by the myriad youtube tutorials out there, is insanely simple, but you would NEVER figure it out yourself. The program is beyond unintuitive.

As for keyframes vs behaviors. . .with all the behaviors, it's amazing how often they don't have something that does what I'm looking for at the time, and I have to create it from scratch. Like almost always.