Indeed. Toys that are made of silicone, some soft plastics or PVC (Jelly) should be stored separately (either in their original packaging or in plastic freezer bags). Glass toys, wood toys, metal toys and hard plastic toys can be stored however you want, but keep in mind that glass toys are breakable and should be stored in padded containers.
Elnoa is correct in stating that many of the soft toys should be stored separately.
However, I'd like to clarify.
Some of the less stable toys can actually melt when stored together...in contact with each other. If you have these toys it is best to store them in individual bags, freezer bags are great. We actually threw away our Jelly and rubber toys several years ago when we realized they were causing infections. They are super porous and there is simply no way to properly clean them.
However toys that are 100% silicone do not have this problem. They are far superior. We store all of our silicone toys in a drawer together. We have a significant collection of silicone toys, Tantus, Vixen Creations, Happy Valley, etc. We have stored these toys loose in a drawer for a couple years with no issues what-so-ever. They are all as good as new.