The reason the game thinks you haven't caught the Pokmon is really stupid and would be easy to fix.
From the Pokmon Go board: galeongirl posted...
Yup, it's the dumbest bug they ever made.
The nearby list checks if you own the Pokemon by searching for the name in the code.
Old pokemon in the code are listed as: WEEDLE.
When a shadow forme is added, they change the name to WEEDLE_NORMAL and WEEDLE_SHADOW.
And, you guess it. The game sees your old Weedles and knows you have not caught a WEEDLE_NORMAL yet, so shows it as uncaught on the nearby radar. Once you've caught a 'new' Weedle with the WEEDLE_NORMAL tag, it'll disappear from the nearby list once again.
You also cannot trade them to Let's Go until they're added to the whitelist. Dumb ass coding.