To be specific in your case, you have to make a mini-league from the results of the three teams which are tied on points (the first criteria).
The matches concerned are:
Round 1: ΠAE 0-1 Bavar
Round 2: Bavar 0-2 Thodoris
Round 3: Thodoris 1-2 ΠAE
Round 4: ΠAE 0-6 Thodoris
Round 5: Bavar 1-4 ΠAE
Round 6: Thodoris 1-3 Bavar
The mini-league ends up as:
Thodoris P4 W2 D0 L2 F10 A5 GD+5 Pts6
Bavar P4 W2 D0 L2 F5 A7 GD-2 Pts6
ΠAE P4 W2 D0 L2 F6 A9 GD-3 Pts6
So, all of you ended up with the same points, now the goal-difference takes effect and ΠAE is the team that loses out.