Css rules ignored
I guess it is related width the bug often reported about IOS9 that might look like Safari is not taking in right account the media-queries.
A possible workaround might be, fixing or adding those values in the meta viewport
:
initial-scale=1.0001
minimum-scale=1.0001
maximum-scale=1.0001
user-scalable=no
Do not set the page width in the meta-viewport! This will just cause more problems.
all in all in this way:
<meta name="viewport" content="initial-scale=1.0001, minimum-scale=1.0001, maximum-scale=1.0001, user-scalable=no"/>
if it works, you may set a javascript just to add a specific meta viewport
for IOS9 webkit only.