Just had new engineered wood flooring put in. The installers left gaps in the floor and filled some of them with wood filler and covered with stain. Is this the protocol....some gaps are very wide. Also, glue everywhere and I don't know how to remove, shouldn't the installers have done that?

Just shooting from the hip here, but it sounds like you got what you paid for.
There shouldn't really be any large gaps with engineered floors, unless they can't get a straight line. And yes they should have cleaned up glue. But start with warm water to try to get it up. If that doesn't work, slowly try solvents. But nothing too harsh.

I don't know if you got what you paid for that is an unfair assumption.

If the product was not defective you shouldn't have gapping issues. However there could have been a defect or possibly the wood was a batch of seconds, or possibly was just not a very good product. Couldn't tell you with out seeing the product.
However your installers should have let you know of any product problems when they saw them. If there is no product failure then your installer failed.

With the glue residue I would call the installer back on that. If it was a glue down, the glue if left on the finish could have eaten into the finish depending on the type of glue. I wouldn't use anything on it just in case they might try pointing the finger at you.

I would call your installer and let them know of your concerns, they should take care of them for you.

Gaps can come from a few different reasons.
1. poorly milled product (manufacture problem)
2. poor subfloor / lack of prep (installer/homeowner)
3. Lack of finesse/ experience/ out of square (installer)

No glue should be on the surface at all , if so dont pay em till they get it off, the glue goes on the bottom not on the face.

sorry, the use of filler although unslightly is normal in small limited amounts. It shouldnt be used to hide poor workmanship. It should be used sparingly to fill nail holes chips corners and the like. Filling a side joint on a beveled floor looks terrible. If the boards dont pull up tight there is a reason, and the boards should have not been installed if its defective.