It probably is, you can try adding either some conditions:
RewriteEngine on
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond $1 !^(index\.php|js|images|robots\.txt)
RewriteRule ^(.*)$ /index.php/$1 [L]
Or include your folder as part of the exclusion (example, your folder is "foobar"):
RewriteEngine on
RewriteCond $1 !^(index\.php|js|images|robots\.txt|foobar)
RewriteRule ^(.*)$ /index.php/$1 [L]