Difference between intermediates and transition states
An intermediate is a short-lived unstable molecule in a reaction which is formed inbetween the reaction when reactants change into products.

Whereas, transition state is just the state before formation of new molecule(involves breaking of bonds of reactants and formation of new ones) 

An intermediate differs from a transition state in that the intermediate has a discrete lifetime (be it a few nanoseconds or many days), whereas a transition state lasts for just one bond vibration cycle. Intermediates may be unstable molecules (in which case they are called reactive intermediates) or highly stable molecules.
The difference between them can be better described through the energy profile diagram.

Transition states are local energy maximums and have partial bonds. This might be one of the reasons why they cant be isolated as intermediates.