This isn't so much an issue as a curiosity, I recently had the problem with the bird flock effect getting stuck in the tree outside of riverwood so I opened the console and disabled the stuck bird, since then I haven't encountered any triggered bird flocks anywhere, did I break something?

Is it Winter time in the game? The birds may have flown South for the Winter.

How many game days have passed? Bird Flocks, like most anything else are random spawns. So, if you are getting random woodland critters spawning, then the bird flock will show up eventually.

I've had that flock get stuck too; that is, after flying off, models still remain embedded in the tree and there is chirping. That aside, you should always be careful when using the console, and whether or not something is a targeted command could have a big influence on your issue.