I've been experiencing a HUGE problem with Lightroom since updating to 5.6. Keywords are not being applied correctly to selected photos. Sometimes they apply to the last selected SET of photos even though I've purposely done a "Select None" and then selected a single photo. Sometimes they are being applied to an entire collection even though the entire collection has not been previously selected. I can usually get the keywords applied to the correct photo (or photos) if I shut down Lightroom and then restart it -- apply the keywords to one photo or group of photos, rinse, repeat. That is highly aggravating. Sometimes that doesn't even work and the keywords either don't apply at all or apply to all the photos in the grid view, whether that is a collection or a folder...
Have you tried deleting the preferences? See Preference and other file locations in Lightroom 5. Note that on more recent versions of Mac OS, you should reboot after deleting the preferences, since the operating system can cache them.
Sprinkling this magic fairy dust often fixes weird LR behavior.
Looks like that might have fixed it. I have to do some heavy metadata work tomorrow and if it did fix it I'll be sure to come back and mark this as a "Correct Answer". Thanks so much.