Chelsea ended their run of three straight defeats with a 1-0 victory over Crystal Palace at Stamford Bridge on Sunday.
Aubameyang, meanwhile, has struggled to make an impact since moving to Stamford Bridge, scoring just one goal in 10 appearances so far.
In Chelsea’s last two games, Potter has opted to play Kai Havertz in attack ahead of Aubameyang and Berbatov feels the former Arsenal striker will be struggling to understand his manager’s thinking.
Berbatov also believes Potter will encounter another problem once Chelsea’s injury worries ease.
‘They needed a win, you can say it was an ugly win but a win is a win and they needed exactly that in this moment,’ Berbatov told Premier League Productions.
‘But they have a lot of questions ahead of them. Firstly, in my mind, they’ve bought a lot of players and what happens when the injured ones come back? They will come back eventually then you have a lot of players, how are you going to deal with that problem, that luxury problem?
‘For example Havertz scored the goal and he’s not the centre-forward. You have a centre-forward on the bench, Aubameyang, and you’re playing someone who isn’t playing that type of position.
‘So now Aubameyang is sitting there thinking, ‘boss, what’s going on? I’m a centre-forward, obviously you don’t trust me.
‘There’s going to be questions flying around the training ground and he’ll need to deal with it. But at the end of the day, the important thing for now was the win for them.’
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