Ah ha! I’m having the same problem with indents. I found the information in this set of posts very helpful.
My problem arose when I compiled my client’s manuscript (after importing it from Word) into a MOBI file for the first time in Scrivener 3, and shock horror, when viewed on my iPad via the Kindle App, the indents disappeared. I used the “as is” formatting option in Scrivener and at first I thought I had misunderstood how to use the “as is” option, having had no problems previously with Scrivener 2, so I went back and fiddled around, and fiddled around, compiled again. But shock horror the MOBI file was still not displaying indents on my Apple Mini iPad, nor on my Apple iPhone 6. So, being a fortunate person with lots of equipment, I had a look at the file via my iMac Kindle App, and there were my indents, displayed in all their beauty. WHAT! So then I loaded my file into my Kindle Touch, and there they were, displayed correctly again. And then … I loaded them into my Kindle Fire, and it too displayed the indents correctly.
Thank you fellow Scrivener users, for this set of post on this topic. Although I’m still stuck with the problem at least I know why there’s a problem, and will not have to compile over and over again thinking it’s me. I’ll work through your solutions, and hope it doesn’t take days to get my indents showing on my iPad via the Kindle App.