I can confirm it happened to me too (PC).
The game had lost connection, and wasn't able to reconnect, despite internet working just fine.
I wasn't able to choose any infamy perk, even though I had some points (at least from having fielded 5 gangers).
When I finished the operation, the infamy screen became inaccessible again (as, I believe, is intended).
Then, I started another operation, and while I could choose two new buildings, I had no infamy at all.
I don't know if it's related to the lost connection, to the new operation, or whatever. But it looks like a bug.
I followed the games advice and played story mode to completion (all 15 missions) before starting custom gang mode.
I now have credit for only for 1/15 in the infamy section when doing a custom gang.
It would appear that a player has to at least start a custom gang before doing story mode to attain all the related infamy points for completing story mode.