They simply consider that it is doctrinally wrong. The matters discussed were the filioque as a doctrine, the filioque in the creed, papal supremacy, azymes, and purgatory. At the council itself, the most difficult doctrines to discuss were the filioque as doctrine, and Purgatory.
Although all the Orthodox bishops present signed the union decree, this isn't everything. Mark of Ephesus and another bishop refused to agree to the council. And also, the Orthodox patriarchs didn't come to the council, but rather sent legates, except for the Ecumenical Patriarch (who died during the council anyway). As such it was needed that the council be adopted by the Orthodox bishops who didn't go, but, aside from a unionist party in Constantinople, this really didn't go well at all. It certainly didn't help that many of the bishops who agreed to the council retracted their approval when they returned home (on particular Gennadius Scholarios) and Mark of Ephesus rallied the population against the approval of the council (not that they were very hopeful about it to begin with).
Florence was not completely fruitless though. Eventually the union was proclaimed in Constantinople by the emperor and the Ecumenical Patriarch, but this didn't erase the anti-unionist party, and this only lasted for 4 months before the city fell for good. The council of Florence has been used as the basis of union with the Orthodox churches that became Eastern Catholic too.
On the matter of doctrine… Catholics believe the Holy Spirit proceeds from the Father and the Son, Orthodox believe the Holy Spirit proceeds from the Father alone. Catholics believe the filioque in the creed was recognized lawfully by the Pope, Orthodox believe only an ecumenical council has that authority. Catholics believe the Pope is orthodox because he is the Vicar of Christ and therefore cannot teach falsehood, Orthodox believe the Pope is the Vicar of Christ only if he is orthodox and therefore he can teach falsehood. Catholics believe both leavened and unleavened bread may be used for the Eucharist, Orthodox believe that only leavened bread can be used. Catholics believe that souls which have no mortal sin but have venial sin or worldly attachment go to Purgatory where they are made perfect before they can enter Heaven through our intercessions for them, Orthodox believe that such souls go to Hell and can be delivered through our intercessions.