Did not see anything in the rule book so hoping someone can help me out.

There are several scenarios that use the remote tokens, are there any penalties for overlapping them or shooting through them?

There is no inherent effect for overlapping or shooting through remotes in general. However, some remotes have specific rules for overlapping them, such as the Buzz Droids from the Discord Missiles upgrade and the DRK-1 Probe Droid.

9 hours ago, abb08 said:

Did not see anything in the rule book

Typically, if you do not see anything in the rule book, then you do not do anything. General rule of "do what the rules say, not what they do not say" applies here. As Ysenhal pointed out, Since the rule book says nothing about overlapping remotes, then, inherently, nothing happens when you overlap them but both (current) standard format remote types have their own rules for when a ship overlaps them.

So unless the scenarios spell out what happens when you overlap the remotes used, then nothing happens when you overlap them.