As I understand from the OP's post the transaction has 2 outputs (txid could be usefull here). It seems like if it was a service fee then it could only be taken from one output after recieving the funds. Sounds like this 0,002 BTC could be sent to the OP's change addresses. SubZeroFish, have you checked all of your addresses?
No, that's not how the Electrum 2FA wallets operate... you need to buy "credits" from TrustedCoin to use 2FA... each transaction you create, uses 1 credit. If you have 0 credits, Electrum will automatically add a payment of either 0.002 or 0.005 (depending on your chosen option) to your transaction, so it creates a 2nd output.
As per the TrustedCoin documentation:
Pay every 20 transactions: 0.0001 BTC/tx 0.002 BTC total
Pay every 100 transactions: 0.00005 BTC/tx 0.005 BTC total
So, if you have 0 credits... and you want to send a transaction for 0.01 somewhere... Your Electrum 2FA wallet will create a transaction that sends 0.01 to X... and 0.002 to TrustedCoin... it then deducts 1 credit... and you're left with 19 credits...
So, the next 19 2FA transactions will NOT have any other 2FA fees added... they will just deduct 1 credit as you have prepaid.