This still seems to be a problem with hunspell version 1.3.3.

The problem can be reproduced by spell checking a file with this one line.

alsdk ✅ sdfkjdsf sldksdfkjsfd

During spell checking, the process list shows:

ispell run -- -- /usr/local/bin/hunspell -a -d en_CA -i UTF-8

The error Emacs (version 25.1.1) reports is:

ispell-process-line: Ispell misalignment: word ‘sdfkjdsf’ point 11; probably incompatible versions

Hunspell skips over the special character when it is run at a terminal prompt.  This is the initial output.

### begin hunspell output ###
        alsdk           File: test.txt

alsdk \~E sdfkjdsf sldksdfkjsfd

 0: Alaska

[SPACE] R)epl A)ccept I)nsert U)ncap S)tem Q)uit e(X)it or ? for help
### end hunspell output ###