The striker and winger travelled back to Merseyside from the Mediterranean after Belgium defeated Cyprus in World Cup qualifying on Tuesday night in a bid to return as quickly as possibly prior to the weekend's Premier League matches.
The Daily Mirror is reporting that Lukaku and Mirallas' £6,500 (per head) bill will not be picked up by Everton as their next match wasn't until Monday night, where they take on Sunderland at the Stadium of Light.
Everton felt it was unnecessary to pay £13,000 for a pair of players who were not due back at Finch Farm until Thursday.
A source told the Mirror: "The Belgium players at clubs in the north-west organised a private jet to fly them home from Cyprus, to get back quicker.
"All the other clubs agreed to pay the £6,500 cost for their players, and Lukaku wasn't happy when Everton told him they wouldn't pay.
"Mirallas was in the same position, and the two of them ended up paying for the flights themselves."