There seem to be some other concerns there, but as it pertains the the flashing tape being lapped properly...that has been done at least proper in terms of lower layer going in first and being lapped thereafter.

What are the other concerns?

Lack of adhesion on the flashing tape (should be rolled with a J-roller), any positive slope to the rough opening sill, drip caps should go on as part of the siding installation, apron flashing installation looks questionable as well.

The roof flashing in the 3rd pic looks questionable as well, same contractor?

Todd different contractor..what can I do? The builder that put windows in is saying that the tape just needs to be under the sill and flange and how he's done thousands of windows.

The window installer is claiming that the siding installer usually flashes the windows. Is that true?

The one installing the Windows would be the responsible party. Usually the house would have house wrap on it at this point then the window installer would tie it all in. There is no way that the sider can flash the sill once the window is in.

Is there a general contractor on this job?

You could peel up the sill flashing slightly at the bottom and tuck the WRB under it and then cap nail it back down.