One of the primary difficulties with reading ebooks is the glare factor. While some ebook readers take this into account and use glare-free screens, other devices (computer and phones, for example) are still not as suitable for ebooks. The glare isn't an issue when reading is done indoors, away from the sun, but it can make outdoor reading less enjoyable and more difficult.
Some ebook readers offer no backlight, which can make reading at night difficult. Those readers that do include a backlit screen make reading at night easier, but backlit screens typically don't hold up well during bright-light reading situations. To offset the difficulty of ebook readers without backlights, some manufacturers have designed special clip-on reading lights for their ebook readers.
Ebook readers do include bookmark functions that allow you to mark your place in a book and return to it, but ebook reading is inconvenient for quickly flipping back to a section. If you are a reader who often gets lost in the story and like to flip back a few pages to refresh your memory about a character or situation, it can be time-consuming to press the "Back" button and try to find the one section you are looking for. There are no page numbers for reference, which means you'll need to do a lot of rereading to find what you're looking for.
The digital nature of ebooks means that text size can be adjusted larger or smaller as needed. While this is a benefit, it can also lead to text being reordered and paragraphs being broken up in odd places. Many ebook readers become accustomed to this, but it can be distracting.
It's hard to discuss a book with someone else who is reading it, particularly if one of you is reading the ebooks and the other is reading the paper version. Ebook readers don't use page numbers, so when a friend asks what page you're on, or when you're discussing a particular section, using page numbers as a reference is out of the question. You can't say, "Remember that scene on page 91 . . ?"