The ePub format has a number of formatting restrictions. When designing documents that may one day be repurposed for ePub output, it's in your best interest to follow some InDesign page layout "best practices".
One such "best practice" is in how capitalization is handled. It's not uncommon for manuscripts to be supplied with all kinds of goofy capitalization of head, subheads and body text. For example, an author may type a heading in a manuscript in any of these forms:
1. The Boy Who Died From Eating All His Vegetables
2. The boy who died from eating all his vegetables
3. THE BOY WHO DIED FROM EATING ALL HIS VEGETABLES
4. THE BOY who died from EATiig aLL HiS veGeTables
This is often "fixed" in the InDesign layout by using the All Caps attribute [command-shift-k (Mac) or ctrl-shift-k (Windows)]. This will cause all the selected text to appear in all caps, but in reality, the underlying text is still the original capitalization, as it was originally typed.
BEST PRACTICE: If text is typed in a goofy combination of mixed upper and lower case, don't just fix it with the All Caps attribute. Instead, use the Type > Change Case command to make the text appear in Title Case or Sentence case, as you want it to appear in the ePub output, and then use the All Caps attribute if you want it to appear in all caps in your print document.
Remember, if you have a lot of capitalization fixing to do, you can add a keyboard shortcut (Edit > Keyboard Shortcuts) to any of the Change Case commands to make them easier to access quickly.