This seems to only happen on interlaced videos, especially some live videos and it never happened on progressive videos such as anime BDs. It occurs when streams change so it will make the beginning or ending of a session silent.
The following is log of the worst rip I've experienced.
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Debug log started at Mon Jan 14 14:34:27 2019 , written by MakeMKV v1.14.2 win(x64-release)
Using 262272KB for read cache.
001005:0000 MakeMKV v1.14.2 win(x64-release) started
001004:0000 Debug logging enabled, log will be saved as C:\Users\Greg Chou/MakeMKV_log.txt
DEBUG: Code 2365587456 at 3tu+2QPU[=7Te!Z9e:29394620
003007:0000 Using direct disc access mode
005053:0308 This functionality is shareware. You may evaluate it for 30 days after what you would need to purchase an activation key if you like the functionality. Do you want to start evaluation period now?
005050:0000 Evaluation version, 30 day(s) out of 30 remaining
DEBUG: Code 2365587456 at 3tu+2QPU[=7Te!Z9e:29394620
DEBUG: Code 0 at z3q2Zsw5q;dm{R\<:213140587
DEBUG: Code 0 at FcF^D,r,a.ZGY1pC:29401014
DEBUG: Code 2147483648 at z3q2Zsw5q;dm{R\<:121265223
DAFD=PAAAADAAAAEABDQkEHgACAQ==
DCE=8v1ydui1bNMnepiwiv1mWhudCg3z7p/nBb0b/NDlfWiteGKyG8P+EYtUCYncaTbC/jbNhEQJhViYJGiknfxFRy7cJ5tV1keSayXnqgNym56xZj6znG7AgmCJplhVBfRcp9wfB5bLXNOTrP6ZNuG8EsJQnlyIRKnf1w==
DCE=vM0OzBOPvMdmOK4FHmzj73Gm0LLexXsCl1ybZZXObimtFwSl1AT7q9Xe7wfR2blcwUSc0q9d6TIdBii20xzO3FDmNwX6S+IVfj0AjLMm2f80/+OYcHgLMFdJYcSmRhN53f34aaPN5hDRt+sF0lK51o+PCO4oK+Xamg==
005085:0000 Loaded content hash table, will verify integrity of M2TS files.
DISCID=FC5844BC9E702E227DB4C1C24C4199909B2C078A
003025:0000 Title #00000.mpls has length of 15 seconds which is less than minimum title length of 20 seconds and was therefore skipped
003307:0000 File 00001.mpls was added as title #0
003025:0000 Title #00001.m2ts has length of 7 seconds which is less than minimum title length of 20 seconds and was therefore skipped
003025:0000 Title #00000.m2ts has length of 8 seconds which is less than minimum title length of 20 seconds and was therefore skipped
003025:0000 Title #00008.m2ts has length of 1 seconds which is less than minimum title length of 20 seconds and was therefore skipped
003307:0000 File 00007.m2ts was added as title #1
001003:0020 DEBUG: Code 233 at PNGPlgQvtNAQo7kwWhJRXjj+:0
001003:0020 DEBUG: Code 233 at c3Rm8P4E4WU9iEDZMZv9O41w:0
001003:0020 DEBUG: Code 233 at 0d5etl39Gr95dfhVY2SaLIwj:0
001003:0020 DEBUG: Code 233 at 5VkNkFJZ0VRI7bbuS7QAgLcA:0
001003:0020 DEBUG: Code 233 at JtxZxwxINQF5HaH6UVmJeiqU:0
001003:0020 DEBUG: Code 233 at 8pWPlbVaF6QtuVK0qEFRSUfP:0
001003:0020 DEBUG: Code 233 at O1hKlTT17ZAM53FOAzNsEw+t:0
001003:0020 DEBUG: Code 233 at ILNNT6y/M24+6S4hfqFLNowM:0
001003:0020 DEBUG: Code 233 at no8SUw/wneLwZipfBvy8I5F/:0
001003:0020 DEBUG: Code 233 at 47QGJK5qc54y7x3SsRokRE3e:0
005011:0000 Operation successfully completed
005014:0000 Saving 2 titles into directory C:/Users/Greg Chou/Videos
DEBUG: Code 256 at D`n#H4_P5x]ysv&d[.a:213132652
DEBUG: Code 512 at D`n#H4_P5x]ysv&d[.a:213132652
004007:0010 AV synchronization issues were found in file 'C:/Users/Greg Chou/Videos/title_t00.mkv' (title #1)
004008:0010 AV sync issue in stream 1,2 at 0:05:31.333 with duration of 3005ms : 601 overlapping frame(s) dropped at segment boundary
004008:0010 AV sync issue in stream 1,2 at 0:09:59.599 with duration of 4905ms : 981 overlapping frame(s) dropped at segment boundary
004008:0010 AV sync issue in stream 1,2 at 0:14:10.954 with duration of 6.01s : 1202 overlapping frame(s) dropped at segment boundary
004008:0010 AV sync issue in stream 1,2 at 0:19:11.253 with duration of 6.61s : 1322 overlapping frame(s) dropped at segment boundary
005005:0080 2 titles saved
005036:0104 Copy complete. 2 titles saved.
Application exited at Mon Jan 14 15:15:46 2019
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This is the only trouble I've met with this software. If it could be solved, this software would be perfect for me!