June 2019
Quirks are, to my knowledge, never properly removed by the Quirk-B-Gone potion. They might not appear in the quirk panel, but they will still be active.
When you consider that Vampires suffer from a similar problem, this makes sense - if a similar system is in use, it will suffer from the same problem.
May 2020
I'm having this issue too and it's 2020. Nice to know that they still haven't fixed it after 2 years. My sim has 5 quirks and I'm not sure whether or not the Quirk-B-Gone potion caused it, but I gained the 5th quirk months after I used the potion.
December 2020
Bug just hit for me too.
I had a quirk that I removed with cheats and added 2 quirks that I generated with the cheats and 2 more where auto generated.
I noticed the UI now shows 5 slots with the first quirk that I removed was red.
After a reload I was back to 4 and added 4 by cheats. Hopefully no more will be generated.