Our Skype English students at Clasesinglesonline.com in Spain make this error a lot. If you just want to say ‘puede ser’ by itself in response to an affirmation, it is much better to say ‘perhaps’, ‘maybe’ or ‘possibly’.
For example, if I say ‘creo que la economia esta creciendo’ and my partner says ‘puede ser’, it is much better to ‘perhaps’, ‘maybe’ or ‘possibly’ since we are expressing doubt. ‘can/could be’ are OK and while you will be understood, it is not very natural. Hope this helps!