Hi,
There may be a couple of reasons for that. In some styles, the actual down-to-the-tic note is not notated "legalistically"
You may want to check the transcription options (Setup/Transcription options) and try out different settings (eg. Standard, Swing, Syncopated) and see how the notation pans out. Also, it will depend on what length the "bleed over" note is as to whether it will get transcribed as a tied-into-the-next-measure note or not. In Notation Composer you can set these parameters to your needs. In Notation Player, it's the "default" setting.
ttfn,
Sherry