If you set your time signature to 3/4 in Notion, then any notes exceeding the rhythmic spelling of the measure, will be flagged in red.
If you have already entered notation into Notion in 4/4 and you then change the time signature to 3/4, you will have to remove the bar lines and add them back. Notion will not automatically bar your music for you. To do this, simply arm your mouse pointer with the select tool, select your bar lines by clicking them, and press "delete" on your keyboard. You can then press the letter "i" on your computer keyboard to arm your mouse pointer with the single bar line. Click in your score to add bars.