Myriad of (relatively minor) issues on my rMBP in the last few days

Not sure how to generalize this, but my rMBP 15" 2014 has started having several weird issues in the past few days:

• Typing freezes (briefly) in Notes


• Searching “Keychain” from spotlight returns some results but NOT “Keychain Access”


• Xcode stops building files because “too many open files on system”, fixed by restart


• Mail autocomplete doesn’t work -> Restart Mail, freezes on open -> Restart again, same -> Open Internet Accounts in System Prefs, freezes -> Restart computer, works


• Beachball opening folder from Dock -> Downloads (about 10 seconds)

None of these issues seems to stay for long. For example, if I search Spotlight for "Keychain" now, it returns the correct result.

More info, I'm running 10.10.1, 16gb RAM, my 500gb hard drive is about 2/5 free. I clean installed Yosemite about 6 months ago too.

Does anyone know this might be? Hardware issue, like failing motherboard or something? Or (hopefully) some kind of software bug?