3.9 updated the tineMCE (Visual) editor. Your plugins or themes may be using code that previously worked on the old editor but may not be compatible with the new editor, and thus you may experience problems.
To figure out the root cause of your issues, make sure to make a backup of your database (you should do this anyway before any changes of your site as a best practice) and then disable all custom themes and disable all your plugins.
Using a default WordPress theme, check to see if the issue is fixed. If not, do a manual upgrade of your WordPress installation.
Then if that’s all working, turn on your custom theme and test to see if everything works. If not, the problem is with the theme – contact the theme developer for support.
If that’s all working, start enabling your plugins one at a time and testing. If everything works, move on to the next plugin. If things break, note which was the last plugin you enabled and contact the plugin developer for support.