Nature Spirit Shamans
 

When making a shaman who uses the Nature Spirit, as soon as they get the True Spirit abilities, HL deletes the familiar and lets you add an animal companion, which is correct, however the new Companion doesn't have the familiar abilities and intelligence that they are supposed to have.

True Spirit Ability

A shaman who chooses the nature spirit as her spirit or wandering spirit gains the following ability upon having access to the true version of that spirit.

Companion Animal (Su): The shaman's spirit animal takes the form of an animal companion of her choice, using her shaman level as her effective druid level. The animal retains all the special abilities and the Intelligence score of the spirit animal, but also has the statistics and abilities of an animal companion. If the animal is dismissed, is lost, or dies, it can be replaced in the same way as a normal spirit animal.

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Lonewolf considers a bug anything that in your eyes doesn't work as intended. So your best bet is to make a bug report about this