I'm not saying I don't believe you, but I can't get my metronome to record if I tried. Something weird must have been going on with your recording set up at the time.
So, in your case, how did you get it to not record? You simply recorded again without changing anything and it was ok? That's weird, too. Things don't usually just fix themselves like that.
Sorry guys. Not trying to be argumentative, but none of this makes sense. You certainly don't have to record a click source on its own track just to be able to record a track without recording the metronome. That would be ridiculous. I, and millions of others, use the metronome to record all the time, and it does not record onto a track. Like I said, I don't even know how to record the metronome onto the same track of my instrument if I wanted to, which nobody ever would.
I'm aware of "Insert>Click source", but that's a whole other, dedicated process.
Turn metronome on, hit record, turn metronome off, listen. It's as simple as that.