On further investigation this only happens (for me) with IE  in windows, and only happens when there is a video preview/still pushed from youtube in flash. I'm using the Webgalli videos plugin V1.5.

Then it's most likely just the video player flash executable (swf file) that's not correctly handled by IE. Instead of executing it it's handled as downloadable file. Do you have the flash plugin installed in IE? If yes, the problem is likely caused by the way the video is embedded in the page by the Videos plugin (oftenly IE needs such kind of things handled differently than any other browser). If the flash plugin is not installed in IE, install it and try again.

Yes that works. I'm not a windows users but I installed the flash player in IE in my parallels test OS and that fixes the problem. Thanks!!!

Looks like its an outdated containers plugin.... hmmm how to fix

Looks like its an outdated containers plugin

Yepp

how to fix

Try ask plugin's author (@ura soul) about it

or try

$bookmark->container_guid = (int)get_input('container_guid', elgg_get_logged_in_user_guid());

in mod/containers/actions/bookmarks/save.php

No, I'm not sure. But the 1.9 page said that most plugins were......

Can I re-assign them manually?

1. Check whether there are newer versions available of those plugins
2. Contact the plugin authors and ask if there are any known issues with Elgg 1.9

Don't rely on a general statement of "most plugins are compatible" regarding 1.9. It depends on every single plugin if it works on Elgg 1.9 without issues. Some plugins really do work without issues and others might only have minor issues or still work due to the BC layer of Elgg. But there are a number of plugins that definitely don't work on Elgg 1.9 and need to be upgraded first. For example for Tidypics there is a new version specifically for Elgg 1.9. For any other plugins released by me I've also published new versions for Elgg 1.9. For some of these plugins the Elgg 1.8 releases might still work on Elgg 1.9 without any noticeable issues but the new Elgg 1.9 releases were specifically tested on Elgg 1.9 to make sure that they work.

If the missing comments are for plugins that already have new releases for Elgg 1.9 I would suggest to install these new versions first to see if the missing comments turn up again. If that's the case the core upgrade has quite likely finished correctly and any comments still missing for other plugins that were not yet ported to Elgg 1.9 are likely to just not being displayed currently due to issues within these plugins.