WARNING: Requested formats are incompatible for merge and will be merged into mkv.

[jajajaime]

This morning when trying to download a playlist that I had some videos of it already downloaded, it gave me the warning "WARNING: Requested formats are incompatible for merge and will be merged into mkv." which created a new file and started downloading it, but I already have that file.
It has never happened to me before.

Here's the verbose output

$ youtube-dl --verbose https://www.youtube.com/playlist?list=PLb3dMxJh3FDF0FFNTfcNxQvPmr1r1yYP8
[debug] System config: []
[debug] User config: []
[debug] Command-line args: [u'--verbose', u'https://www.youtube.com/playlist?list=PLb3dMxJh3FDF0FFNTfcNxQvPmr1r1yYP8']
[debug] Encodings: locale UTF-8, fs utf-8, out UTF-8, pref UTF-8
[debug] youtube-dl version 2015.11.27.1
[debug] Python version 2.7.10 - Darwin-14.5.0-x86_64-i386-64bit
[debug] exe versions: ffmpeg 2.8.2, ffprobe 2.8.2
[debug] Proxy map: {}
[youtube:playlist] PLb3dMxJh3FDF0FFNTfcNxQvPmr1r1yYP8: Downloading webpage
[download] Downloading playlist: LEGACY OF THE VOID - FULL CAMPAIGN
[youtube:playlist] playlist LEGACY OF THE VOID - FULL CAMPAIGN: Downloading 13 videos
[download] Downloading video 1 of 13
[youtube] s4BTOLpknLY: Downloading webpage
[youtube] s4BTOLpknLY: Downloading video info webpage
[youtube] s4BTOLpknLY: Extracting video information
[youtube] s4BTOLpknLY: Downloading DASH manifest
[youtube] s4BTOLpknLY: Downloading DASH manifest
WARNING: Requested formats are incompatible for merge and will be merged into mkv.
[debug] Invoking downloader on u'https://r18---sn-q4f7sney.googlevideo.com/videoplayback?id=b3805338ba649cb6&itag=299&source=youtube&requiressl=yes&nh=IgpwcjA0LmRmdzA2KgkxMjcuMC4wLjE&pl=22&mv=m&ms=au&mm=31&mn=sn-q4f7sney&ratebypass=yes&mime=video/mp4&gir=yes&clen=930550035&lmt=1447456818075521&dur=1982.183&fexp=9407053,9408490,9408710,9416126,9417683,9418204,9420452,9422342,9422434,9422541,9422596,9422618,9423662,9423992,9424037,9424048,9424473,9424617,9424963,9424988&key=dg_yt0&signature=967DD066E5613F2959C169D1956F5F8F143D3CBB.4526F6B979F717DE177E2C07FAE7EE72B97ADB7E&sver=3&upn=vmfA0yQrPFY&mt=1448982875&ip=68.66.86.94&ipbits=0&expire=1449004560&sparams=ip,ipbits,expire,id,itag,source,requiressl,nh,pl,mv,ms,mm,mn,ratebypass,mime,gir,clen,lmt,dur'
[download] Destination: LEGACY OF THE VOID - Episode 1 - Entire Campaign - FOR AIUR & THE GROWING SHADOW-s4BTOLpknLY.f299.mp4
[download]   2.3% of 887.44MiB at  6.20MiB/s ETA 02:19

[dstftw]

This is expected behavior when bestvideo and bestaudio are different containers.