If I click the lightning bolt emoji and then press the enter key, this bug shows up where there are missing emoji's from recently used (please see screenshot).
It happens on here, I haven't tried it on a different installation yet but assuming it'd likely cause it there too.
I don't think I'm able to reproduce this, though I'm a little confused by your description of events, specifically when it comes to the 'and then press the enter key' part.
The following was recorded with Firefox 68. In it, I open the smilie/emoji menu and click some icons then watch them appear in the 'Recently used' area - but hitting the enter key doesn't appear to do anything of interest, so perhaps I'm missing something that you're doing?
It seems this only happens to the lightning emoji that I've seen.
Here are the steps I did:
1. Start typing in the quick reply area.
2. Go to emoji's and select the emoji.
3. Press the enter key right after the emoji in the quick reply area.
4. Go back to the emoji recently used area, and you'll see something similar to my screenshot. (Reproduced in Google Chrome as well).