What are the main problems of steganography?

The biggest problem steganography faces is that of size. There is a limit to the size of a file which you can embed information into.

For instance if you take a 16 bit image where each pixel is 4 bytes in three colours RGB you can only reliable encode the lower byte before the colour changes become visible in the viewed image.

This means that the image you are embedding your data in has to be 1 quarter larger than the encrypted data itself.