When I get bonus heros their not even the ones I have favorited. I just get random heros which kinda defeats the purpose of picking which cards we want to receive.
Welcome to the forum 
Sounds like you should open a support ticket here: https://d3go.com/mobile-games-support
I recommend being more specific and explicit than your post. What favourites have you picked? What bonus covers have you recieved? that sort of thing.
I am having the same problem.
I chose Kate Bishop, Spider-Gwen, and Gwenpool as my bonus characters (by clicking on the gold star).
Today I got my first bonus cover and it was for Scarlet Witch. The strange thing was that the initial cover I drew was also Scarlet Witch. So both the original cover and the bonus cover both happened to be Scarlet Witch.
Scarlet Witch has not been favorited by me, and she doesn’t have a gold star on her cover profile.
I’d like to buy some covers from the current PVE vault, but I’m not going to if the bonus covers I have a chance of getting aren’t even the ones I picked.
Finally got my first bonus hero- also one I had not selected. I chose 4* Carol Danvers, war machine and 5* thanks. Got a 3* Captain marvel. Not what I was expecting from this new bonus feature
The bonus cover will be the same star level as the drawn cover. If you only “favorite” 4-stars and you pull a 3-star, the bonus cover will be a random 3 because you have no “favorite” 3s.
Additionally, bonus heroes don’t apply to the vaults. Standard, Elite, Heroic, and Legendary draws can all drop bonus heroes, as can non-vault event tokens (release PVE and most PVP tokens).
For best results, choose one character from each rarity as a favorite to get that one powered up efficiently.
Here - read this. It will explain everything you need to know.
Hello everyone, I have a major question and I understand how the bonus hero pulls work. But!?!
Do you get a bonus hero (every time) you pull a 3 star character with recruit tokens?
Ex: Using a recruit token and pulling a 3 star Strange and having 3 star cover hulk selected/favorited in roster. Will I pull a bonus hero hulk?
I have been getting bonus heroes when it started, then I updated yesterday and now I’m not getting bonus heroes when I pull 3 star covers from recruit tokens; I fear the update has screwed up my bonus heroes. Just like I don’t get ads and bonus/intel anymore. 
P.S. I am playing on a Kindle Fire Tablet.
The only token that guarantees a Bonus Hero is the Standard token, and then only when you pull a 3* hero from one (which is very rare). All other tokens have a straight 5% chance of awarding you a Bonus Hero if you pull a 3*, 4* or 5* from them.
Scarlet Witch is a 3 Star…When you get a bonus hero it’s the same Star amount
if you have no selected 3 Star BH and you get a 3 Star bonus hero rng picks one for you