how did I get apple tree seed?

[NeverDark]

only Bird's nest？
help

[Huillam]

Thieving is another option: both the Merchant and Bob the Farmer have the seeds.

[Quisty]

I don't think you can get them from Bird's Nest, only Bob the Farmer & Merchant. At 1/500 (0.20% chance) per pickpocket.