So last night I was at an event and my camera had a hard trying to focus. Does anyone have any tips? It was a little dark but I've shot in darker places with my a99 with no problems. I did have it on phase detection so maybe that had something to do with it?  I also would change my settings from AF-S to AF-C or from center to flex spot. Nothing seem to help.

There is a red focus assist lamp that you can turn on or off to help.

One of the FIRST things that I did is to turn off the autofocus on the shutter button and have one of the buttons on the back become the autofocus button.  The reason is simple.  Most of the time the subject isn't moving out of the focus plane enough to require refocus.  The default setting makes the camera focus each and every time you're taking a picture.  Why refocus when it's not necessary, especially in hard to focus conditions? That... and auto focusing drains the rather short life battery even more.

https://www.youtube.com/watch?v=NscdKnP4c08

There's some weirdness going on with the A7RII’s focusing as well. If I remember the DPReview article correctly, they said that it focuses using the selected aperture - unlike a DSLR, which holds the lens open for focusing, but is limited to f/2.8 for AF point sensitivity. So according to the article (assuming I'm remembering correctly), if you shoot wider than 2.8, AF speed will be faster than your A99; as you stop down, the A99 will stay the same speed, but the A7RII will slow down.

If you were shooting at f/8 with flash, that would explain it.

Or maybe it was one of the settings mentioned above.

When mine is having issues focusing in low light, I'd use the focus area big enough to cover their faces.  I'm usually at Flexible Medium.  Though, I may go to Flexible Large; or just Center.  I keep on Phase Detect.

I shoot a lot in low light and often shooting a moving subject while I'm moving.

I've used a 1D4, a 5D3 and an A7s, and the conclusion I've come to is that there's no AF system that's adequate for my low light shooting needs.

I've found shooting manually is far faster and more accurate. I either use zone focus or I mark the lens with something I can feel and set it for what I estimate is 10 feet and use that as a starting point. Then I give a little twist for closer or further. It takes a few minutes of practice/warm up, and then it's a lot easier than you'd imagine.