Apart from the grain issues already mentioned and which can be worked around, the only other thing I can think of is dynamic range.
Unless you are working with a top quality film scanner, you may be reducing the dynamic range present in film by scanning it. This is actually one of the most compelling reasons to use a dedicated film scanner as opposed to a flatbed.
Another thing to keep in mind is that output of the scan should be kept at 48-bit colour (each colour represented by up to >65000 different levels) until at least all desired target colour balance is achieved.
In principle, you should strive for good colour balance straight out of the scan process, by balancing the scan lighting itself.
Some scanners don't allow that, which means you got to do it after the scan. That's called "post-processing".
If you are working with only 24-bit colour output (where each colour is represented by only 256 distinct levels), you post-processing colour balancing might be limited.
There are extensive technical explanations for this.
Suffice to say you will observe banding of large colour gradients if you apply any extensive colour re-balancing to a 24-bit colour image.
This is NOT to say ALL your colour has to be handled at 48-bit! Only up to the point where you are done with colour balance corrections, for whatever reason you might undertake those.