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I ripped a blu-ray and the video output has ripples(example attached) whenever there is a lot of motion.

This is common when ripping high-resolution scans of prior DVD output. There are half-frames that would be displayed in alternating scans, but they've been combined into full frames that get displayed at a slower frame rate (24 frames per second instead of 60 half-frames).

Supposedly, it should have been fixed before the disk was written, but...

Is there a setting in MakeMKV i can change to make these go away?

If it's conversion from DVD to BD, no, there isn't. The disk is encoded with the ripples. A lot of old TV stuff is like this.

If anyone stumbles upon this with the same/similar issue and are encoding outside of MakeMKV I was able to fix it by playing with the de-interlacing settings in my encoding software.

Just for future reference, providing some technical detail about the file in question would be extremely helpful.

There's a small program called MediaInfo that gives a host of information such as the bit rate, resolution, frame-rate, color system (NTSC/PAL), scan type (Interlaced/Progressive), and so much more. All of this will be useful when diagnosing problems like this.

One thing to bear in mind is that the resolution displayed by MediaInfo may not be the true frame size, it's actually set when authoring the disc and I believe there are some constraints involved. For example, NTSC DVDs seem to mostly be set at 720x480 when in reality they rarely are. 16:9 NTSC frames are more likely to be 853x480 and 4:3 NTSC frames are probably 640x480. I've read that the 720x480 dimension was the old NTSC DTV standard in 3:2 aspect ratio, but why they chose that setting for all NTSC DVDs I have no idea.

To see the true frame dimensions you can drop the file into the "Info tool" tab of a program called MKVToolNix, which will give accurate "Display" dimensions. And, of course, most video editing suites will give the same accurate information.