For anyone seeing this issue on SilverStripe 3.1, I used the following code in my .htaccess to resolve the issue (as suggested by lestatron)
### SILVERSTRIPE START ###
<Files *.ss>
Order deny,allow
Deny from all
Allow from 127.0.0.1
</Files>
<Files web.config>
Order deny,allow
Deny from all
</Files>
# This denies access to all yml files, since developers might include sensitive
# information in them. See the docs for work-arounds to serve some yaml files
<Files ~ "\.ya?ml$">
Order allow,deny
Deny from all
</Files>
ErrorDocument 404 /assets/error-404.html
ErrorDocument 500 /assets/error-500.html
<IfModule mod_rewrite.c>
SetEnv HTTP_MOD_REWRITE On
RewriteEngine On
RewriteRule ^vendor(/|$) - [F,L,NC]
RewriteRule silverstripe-cache(/|$) - [F,L,NC]
RewriteRule composer\.(json|lock) - [F,L,NC]
## Add these two lines to fix adding ?url= to urls where folders exist (e.g. like /blog)
RewriteCond %{REQUEST_URI} ^/([\w_-]+)([^/]{1})$
RewriteRule (.*) %{REQUEST_URI}/ [R=301,L]
RewriteCond %{REQUEST_URI} ^(.*)$
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_URI} !\.php$
RewriteRule .* framework/main.php?url=%1 [QSA]
RewriteCond %{REQUEST_URI} ^(.*)/framework/main.php$
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule . %1/install.php? [R,L]
</IfModule>
### SILVERSTRIPE END ###