It is not possible to delete a single blueprint from a difficulty/faction combination in the Wave AI manager.
How to reproduce:
1) Open Wave AI manager
2) click "add".
3) add 2 blueprints for the comabination faction -1 and difficulty 1 and click "ok".
4) click "edit" for this combination.
5) click "del" for 1 blueprint. The blueprint will disappear. Then click "ok".
6) click "edit" for the same combination. The combination still contains 2 blueprints.