If you imported your project via MusicXML, then it’s certainly possible for you to end up with a different disposition of voices than if you had input the music yourself directly in Dorico. You can sort it out relatively easily, though: I suggest you switch on View > Note and Rest Colors > Voice Colors, which will help you to show where different voices are being used. You can work your way through the flute part selecting a passage at a time, then choosing Edit > Voice > Change Voice > Up-stem Voice 1.