I went exploring with pet #107541, and of the 11 items I found, I could only pick up six (as I had more than 999 of some of the items) and only those six were counted in the Research Achievements. Shouldn't this be the same as with the visited buildings though - all items found by a pet get counted for the "collect 50 different items" requirement? Because even if you're not the right GP for the hero-worshipper building or if you choose to not fight the temple guardian, those still get counted as 'visited' buildings.

While it does say "collect" items, shouldn't the items you come across but can't pick up still get counted towards the total, especially considering the new item limit?

I agree. It's also rather limiting if your throdamas don't yet have their harvester pheromones.

You should have posted this under suggestions though because so far as I know this isn't a bug.