This is not normal, but is something that tends to happen
a lot. While there are some followers who join you regardless of your Charisma and party count, all three you currently have check your follower limit before joining.
For some reason, when a follower joins you for the first time (which requires that you have space for them in your party), the game sometimes doesn't register them as taking up a follower slot. In your case, my bet is on Magnus since I've had him as a "freebie" before, but it
could be Virgil. Because the glitched follower does not count towards the party limit, you get to recruit one more person after your party is technically full.
So, normally, Jayna should have complained that you have too many people with you already and refused to join, but it's very likely she isn't the problem here.
You can, if you want, find the culprit by having your followers (one by one) wait and then immediately join back. The one who refuses to join after that is the extra one. Save beforehand if you want to keep exploiting the glitch.