Trouble with Animal Companion Levels
 

I just started using Hero Lab to build a hunter. She's at second level, but her animal companion is one level higher at third.

From the animal companion page on d20pfsrd.com

The character’s druid level. The druid’s class levels stack with levels of any other classes that are entitled to an animal companion for the purpose of determining the companion’s statistics.

Why does Hero Lab do this? Is there something I'm missing?

I'm not seeing anything wrong with this.

The Hunter says it functions as the same as the Druid.
With a 2nd level Hunter or a 2nd level Druid, the animal companion for either is a 3 hit die creature from the appropriate list.

The animal advances based on the druid's level.

You're starting with a base creature, from an approved list.
It looks like they're all (just tested three) of three hit dice to start.

Just like Ualaa said, a 2nd level animal companion will be 3 HD. They receive 2 HD at 1st level, and then 1 additional HD at 2nd level. Animal companions also don't advance 1 HD every Hunter level. There are some levels where the additional HD is skipped. For example, the companion will not advance a HD when the character advances from 6th to 7th level.

Familiarize yourself with the chart on this page. It should help make things clear.
https://www.d20pfsrd.com/classes/cor...mal-companions