Ally Financial Banking Wrongly charged for penalties and late charges, due to their mistakes.

Ally then claimed to have taken $4.94 less than the contracted amount,
This isn't a claim open to interpretation. You can either prove or disprove this by looking at your bank statements compared to the contract. So did they take less than the amount required?

Unauthentic looking letter in mail states the late fees?
Again this was or was not an authentic letter is not open to interpretation. If you called Ally and they admit they sent the letter then your opinion on the "looks" isn't an issue, and the fact is that it was authentic.

Called company to discuss, they take no ownership in thier mstakes.
- What Mistake? When you set up the Auto-Pay did you verify that the correct amount was being taken out? Did they magically change this amount? Do you get monthly statement and did any of them ever show you were short?

Amount of late fees charged in unauthentice looking vs. Ally's late fee charge was inconsistent with letter rec'd.

 How was it inconsistent? Is the letter asking for less late fees? More late fees? Is the letter including the shorted amount?

Regardless of the reason if you have been paying $4.94 less each month, you would be required to pay at least that past due amount. As for any extra fees or interest you may be able to fight it, but it really depends on what the full circumstances are.  As we are only getting one side of the story here.

Good Luck