Phone the number with this script (withhold number or get your own burner!):
"Hello, this is Sharon from EE. We have had a case of potential fraud registered against the top-up payment made on this phone on June 2nd, as the name on the card does not match the name that this phone is registered to. Before we can look into this further, for security, please can you confirm your name?" <pause for answer> "Thank you, and your date of birth?" <pause for answer> "Thank you. Now please can you confirm your relationship to the card holder?"
Could be any number of responses to that. He's my dad, I'm his girlfriend, he's my boss, he's my workmate etc
Next question will be "and can you confirm that you had the cardholder's permission to use their card?"
You may get some more background here like; Yes, he tops it up himself as it's a work phone and reclaims it through expenses, or, yes, I don't have a card so I give him cash and he tops my phone up for me as a favour.
Then just finish with "Thank you for confirming that. I'll remove the fraud flag from the account"
You should have all the answers you need at the end of that. If it's innocent, breathe a sigh of relief and forget about it. If it's not, you have her name and DOB so go and do some digging before you confront him.