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Having issues with the third disc of season 5 of Dexter. There are 4 episodes on the disc, and the second two fail with errors.

Saving 4 titles into directory K:/Mkv output
Error 'Scsi error - MEDIUM ERROR:L-EC UNCORRECTABLE ERROR' occurred while reading '/VIDEO_TS/VTS_05_1.VOB' at offset '1482301440'
Error 'Scsi error - MEDIUM ERROR:L-EC UNCORRECTABLE ERROR' occurred while reading '/VIDEO_TS/VTS_05_1.VOB' at offset '1482301440'
DEBUG: Code 0 at Y|IF&],tF&yI9BW_ayAs:121263038
DEBUG: Code 0 at GY@CNuI|Nl;96U@'3lN:121261750
DEBUG: Code 0 at Y|IF&],tF&yI9BW_ayAs:213130559
DEBUG: Code 723780 at Y|IF&],tF&yI9BW_ayAs:29393286
Error 'Scsi error - MEDIUM ERROR:L-EC UNCORRECTABLE ERROR' occurred while reading '/VIDEO_TS/VTS_05_1.VOB' at offset '1482301440'
Error 'Scsi error - MEDIUM ERROR:L-EC UNCORRECTABLE ERROR' occurred while reading '/VIDEO_TS/VTS_05_1.VOB' at offset '1482301440'
DEBUG: Code 0 at Y|IF&],tF&yI9BW_ayAs:121263038
DEBUG: Code 0 at GY@CNuI|Nl;96U@'3lN:121261750
DEBUG: Code 0 at Y|IF&],tF&yI9BW_ayAs:213130559
DEBUG: Code 723780 at Y|IF&],tF&yI9BW_ayAs:29393286
DEBUG: Code 0 at dTY}Ut\3Z+1[99lR]yBK&:29398967
DEBUG: Code 0 at dTY}Ut\3Z+1[99lR]yBK&:29398967
LIBMKV_TRACE: Exception: Error while reading input
Failed to save title 1 to file K:/Mkv output/title01.mkv
Error 'Scsi error - MEDIUM ERROR:L-EC UNCORRECTABLE ERROR' occurred while reading '/VIDEO_TS/VTS_06_1.VOB' at offset '504115200'
Error 'Scsi error - MEDIUM ERROR:L-EC UNCORRECTABLE ERROR' occurred while reading '/VIDEO_TS/VTS_06_1.VOB' at offset '504115200'
DEBUG: Code 0 at Y|IF&],tF&yI9BW_ayAs:121263038
DEBUG: Code 0 at GY@CNuI|Nl;96U@'3lN:121261750
DEBUG: Code 0 at Y|IF&],tF&yI9BW_ayAs:213130559
DEBUG: Code 246150 at Y|IF&],tF&yI9BW_ayAs:29393286
Error 'Scsi error - MEDIUM ERROR:L-EC UNCORRECTABLE ERROR' occurred while reading '/VIDEO_TS/VTS_06_1.VOB' at offset '504115200'
Error 'Scsi error - MEDIUM ERROR:L-EC UNCORRECTABLE ERROR' occurred while reading '/VIDEO_TS/VTS_06_1.VOB' at offset '504115200'
DEBUG: Code 0 at Y|IF&],tF&yI9BW_ayAs:121263038
DEBUG: Code 0 at GY@CNuI|Nl;96U@'3lN:121261750
DEBUG: Code 0 at Y|IF&],tF&yI9BW_ayAs:213130559
DEBUG: Code 246150 at Y|IF&],tF&yI9BW_ayAs:29393286
DEBUG: Code 0 at dTY}Ut\3Z+1[99lR]yBK&:29398967
DEBUG: Code 0 at dTY}Ut\3Z+1[99lR]yBK&:29398967
LIBMKV_TRACE: Exception: Error while reading input
Failed to save title 2 to file K:/Mkv output/title02.mkv

There is one scratch near the outside edge of the disc that runs with the curve, roughly a third of an inch. I cant imagine that ruins half the disc though.. any ideas?

Unfortunately, scratches don't have to be obvious to cause problems. And some you can see might actually be invisible to the laser!

Disks are read from the center outward, and the amount of data per track increases as you move away from the hub. Scratches that run spiral affect more data than ones running radially.

If waxing the disk does not make it readable, you will probably need to have someone with the proper equipment resurface it, or borrow another copy from someone.