Hello there,
after I searched hours on the internet to solve this problem, I couldn't find anything that would solve it. At first I started a new game and raised fishing to level 3 and I could fish with bait. But I didn't want to start all over again. So I copied my savefile, turned the testingcheats on and tried a few things to solve it on my own. I let another Sim train the fishing skill to level 3 and wanted to choose a bait, like expectated, it didn't worked. I removed the Fish spawner (on accident) and tried to fish again with bait. It worked, it seems like you can fish with a bait if you don't click on the fishspawner. Then I catched some goldfishs at the park and placed them as a new spawner, and again I was able to catch with bait. I catched a few more and placed them on an existing spawner, catch with bait works like usually. So it seems the problem is that the spawners need to be updated with another fish.
Tl:dr
Place a new fish in the spawner and you can fish again.
The Idea to just buy just came in my mind. So buy ten goldfishs or something at the store and place them on the spawner where you wish to fish.
You also can buy a few more, put them in the fridge and put them in your inventory if you want to fish on a new spawner.
Tested with vanilla sims 3, no Add-ons, no Mods, version 1.38.
Hope I could help. Let me know if it worked for you, just being curios.