boars always spawn in the first biome. even near bases. its just random. workbenches nearby disable all spawns. but nothing prevents you from removeing these.

did you stay near it till it was 61%?`if you leave the area animals can despawn sometimes.
or break out of thier pen. OR GET KILLED by something else when the player is nearby.

nightspawns can also disappear upon dawn.

but boar tameing is currently not really worth it anymore. chickens are just too good compared and alot easier to manage. none of the boar materials are used for any endgame meals anymore either. same for wolfs and lox but these can atleast be used for base defense compared.