Currently, at least when using nvenc/nvdec, Plex seems to deinterlace interlaced content (like 1080i, 480i, etc.) by simply throwing half of the temporal motion away. For example, 1080i 30 is transcoded to 1080p 30, where it should be transcoded to 1080p 60. (Each interlaced frame contains two fields - effectively two frames.)
Please use yadif=1 (Output one frame for each field), or the appropriate equivalent for the given hardware decoder, like yadif_cuda, so full motion of interlaced material is retained.
This issue is especially noticeable when playing Live TV or DVR recordings.