` is used to create an inline code block. Instead, use \code, \endcode rather than a markdown code block.
for example
\code
this is an inline `code block with ` characters
\endcode
renders with the ` characters included.
When a pair of `s is encountered in the code, doxygen will not process whatever is between.
The following will render correctly:
\code
for file in `ls dir/*.filter`
do
done
\endcode