It will be easiest for folks to help you if you create a reproducible example (reprex).
A few thoughts:
Regarding #1
If attempting to filter for equality with "?" doesn't seem to work, my guess is that there is other data in the field which is keeping is making the conditional always true. This could be whitespace characters like spaces or tabs or non-printable characters. If you find a row with a "?" in it you could see how many characters are using nchar function.
Regarding #2
It depends on exactly what you want, but you could ensure that column is a character column to being with by using the stringsAsFactors = FALSE is used when you're reading data into your dataframe.