Ok it works after long searching trip, here what i did:
1- Download latest FFMPEG from here (this was causing alot of problems for me).
2- Add the subtitle to the input files:
ffmpeg -i "input.mkv" -i subtitles.srt -c copy -c:s srt -metadata:s:s:1 language=eng -map 0 -map 1 -map_metadata 0 output.mkv
3- Cut the parts you need as you did normally ffmpeg will cut subtitle stream also
ffmpeg -i input.mkv -ss 00:00:00 -t 00:01:35 -c copy -map 0:0 -map 0:1 -map 0:2 -qscale:0:V 0 -y out0.mkv
4- Join the cut files using concat demux:
ffmpeg -f concat -i mylist.txt -c copy output.mkv
where mylist.txt contains:
file out0.mkv
file out1.mkv
And enjoy :).