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In the creator's commentary it states that Overwatch follows the normal rules for shooting.

My gaming buddy therefore says that I can't fire overwatch at a character that charges, but is behind a bubblewrap because you can't target characters if there is a unit in front of the character.

Is this the right interpretation?

Well, as he is charging he will have to go through/around the bubblewrap. Just tell your opponent that you are waiting until his character clears the bubble wrap unit, then firing overwatch on him.

Overwatch is resolved at the spot the character is placed at the beginning of the charge (See the LOS ruling in the commentary)

Your buddy sounds like a fun guy to play with.

Your buddy is right
You cannot Overwatch as the character is no legal target.
This also applies if a unit is behind LOS blocking models/terrain (no line of sight = no overwatch) or starts their charge move outside the range of the weapon

 master of ordinance wrote:
Well, as he is charging he will have to go through/around the bubblewrap. Just tell your opponent that you are waiting until his character clears the bubble wrap unit, then firing overwatch on him.

suggesting to use house rules is not the really an answer to the question

 kodos wrote:
Your buddy is right
You cannot Overwatch as the character is no legal target.
This also applies if a unit is behind LOS blocking models/terrain (no line of sight = no overwatch) or starts their charge move outside the range of the weapon

Shooting prevents targeting of Characters, no target is selected in overwatch. You can shoot at Characters that charge, unless they cannot be seen.

Plus, the Character rules say he can't be chosen as a target in the Shooting phase if he isn't the closest enemy unit. Overwatch doesn't happen in the Shooting phase.

 doctortom wrote:
Overwatch doesn't happen in the Shooting phase.

this is not an argument as Overwatch says:

Overwatch is resolved like a normal shooting attack (albeit one resolved in the enemy's Charge phase) and uses all the normal rules except that a 6 is always required.

But I can see the argument that Overwatch does not choose a target because it is triggered by the attacking unit
but than the FAQ say:
Note however that the unit being charged still obeys the normal rules for targeting when it fires Overwatch