Additional Charges Weeks After Holiday - RIP OFF

Received car rental as part of a holiday package through Thomson Holidays. The package included basic car and cover for 14 days. When I arrived at Sanford International airport 14/06/14 there was only a short wait before sorting my car details etc. at Alamo car hire. After speaking to a member of staff I chose to upgrade from 3rd party just in case of an accident. I was told because I paid for additional insurance I could have a free upgrade car. This was great I received a much better model car and had comprehensive insurance. Now the bad part. When returning the car it was a simple process. The keys were just handed back to the attendant who signed the car off with no damage etc. A few days later I checked my bank to see if my additional upgrade charges had been taken out. They were but so was an additional £39.82. This was confusing as I paid the additional fuel charge to bring the car back without a full tank, and the car was also signed off as non-damaged. These were the only additional charges I could receive on my contract. I emailed Alamo asking why ? Yet still a week later I have received no response. To add insult just under two weeks after arriving back home I check my bank again to see that an additional £3.63 had been taken out by Alamo.. Why ?. I paid cash for all toll roads and there was no electronic tag in the car, so I cannot possibly understand the additional charges. Rip Off be aware.