However, after Rebic's hat-trick in Eintracht's 5-3 win over Waldhof Mannheim in the first round of the DFB-Pokal, Hubner said: "We are still optimistic."
Rebic was the hero away to the 3.Liga side on Sunday, scoring three goals in 12 minutes as Eintracht came from behind to win.
Mannheim led 2-0 after 11 minutes and 3-2 with 18 minutes remaining before Rebic's three-goal haul.
The ex-Fiorentina attacker's equaliser came in the 76th minute with a clinical finish from inside the six-yard box.
Four minutes later, Rebic secured the lead for Eintracht, finishing off good work from Filip Kostic to calm the travelling fans.
He earned his hat-trick and sealed the victory with two minutes to play, tapping in another goal from close range to seal Eintracht's progression to the second round.
Asked about Rebic, Eintracht head coach Adi Hutter replied: "It's always an individual situation for each player.
"If someone has the opportunity to go to a top club, it will be difficult to keep him at the club."
Rebic has flourished since arriving from Serie A on an initial loan deal in 2016, scoring 17 Bundesliga goals and 25 in all competitions.
He is expected to cover the loss of goals from Jovic and Haller - who combined struck 32 times and created 15 assists during the 2018-19 Bundesliga campaign.
Rebic has 28 caps for his nation and has scored three goals at national team level, with his most important strike coming against Argentina in the group stage of the 2018 World Cup.