FileVault blocking macOS Sierra upgrading process from OS X El Capitain
It may be paused... Look in diskutil cs list output for "Conversion Progress" near the bottom.

Conversion Progress:   Paused


If it says "Paused" like above then on 10.11 you can use fsck_cs to fix it. Use the Physical Volume disk id from your diskutil output (disk0s2 in this example):

fsck_cs -y disk0s2