BuddyPress.org

Well,I had seen this issue so many times,so I experimented.

If your plugin is activated sitewide(which is almost true in case of buddypress) ,It is going to give you at least one such error(try with other sitewide activated plugins by upgrading them).

So this is not an issue with the buddypress but the problem is with the updating/activation of site wide activated plugins in wpmu as far as I see.

Easy work around(if you don’t want to see this problem)

1.Login to dashboard

2.deactivate buddypress

3.upgrade buddypress

4.Activate again

You will never find this problem again.