While I was creating characters when I first started the game I noticed that one of the portraits (the female pink spikey hair one) that one of the pre-made characters was using was not showing up in the portraits list. I assumed it was just bugged and moved on. Today however, I went to reroll my party since I made a few mistakes creating it and when I loaded a saved version of one character her portrait (the long haired one with goggles and face mask) had turned into a screenshot portrait and the previous portrait had also disappeared from the list, which really irritates me since I was using that one.

Anyone else had issues with the handdrawn portraits that should be there not being there?

Not exactly, but I had one issue being the character's portrait of Hex suddenly turning into the one of Pills, and I fixed it by editing C:\Users\<yourname>\Documents\My Games\Wasteland2\Save Games\<yoursavegamename>\<yoursafegamename>.xml and replacing
<name><@>Hex{F}</name><displayName><@>Hex{F}</displayName><portraitName >wl2_portrait_Pills</portraitName>
with
<name><@>Hex{F}</name><displayName><@>Hex{F}</displayName><portraitName >wl2_portrait_Hex</portraitName>

Please don't do anything if you don't know what your're doing and stuff :D