I noticed my pet dps ratio on a single target fight would have the pet basic attack damage and melee damage would be pretty even like 35%. But when I look at some of the hunter top logs on WOL their pet melee damage would be a lot higher like 40%+ compared to the pet basic attack which would be under 30%.
Are you using the Glyph of Stampede(copies your current pet rather than calling everything from stable)? Also other Hunters might have AoC where as you don't(higher Stampede uptime).
This seems to be the explanation. If you look over those logs again, you will probably notice that on logs where the Melee damage is very high (~45%+) WoL only sees one pet; all the Stampede pets are getting rolled into the main pet. On the other hand, logs where Melee damage is normal (~35%) are logs where the hunter is not using the glyph.
It's a minor glyph, those are, as far as I'm aware, never either a DPS increase or a DPS loss.
Well, so there was a period of time where the copied pets didn't get to cast Rabid because they were copies, so it was a loss. But IIRC they took the ability of Stampede pets to cast Rabid out anyway so that's probably no longer a concern.