• Have you checked if problem occurs with fish 2.4.0?
• Tried fish without third-party customizations (check sh -c 'env HOME=$(mktemp -d) fish')?

fish version installed (fish --version):
fish, version 2.4.0

OS/terminal used:
macOS 10.12.*
iTerm2 3.*

The prompt selection is including an extra character (the one in front of the cursor).

Reproduction steps

1. Setup:

function fish_user_key_bindings
  bind \ce begin-selection
  bind \cr kill-selection
end

2. Place the cursor somewhere except the beginning or end:

3. control+e then left or right

4. control+r

Results

After left:

After left kill:

After right:

After right kill: