Hi there,

Check the growth of the strain on the same medium lacking 5FOA.

Is it about URA3 excision alone or associated with an other gene?

Your answer is in this document.

https://www.sciencedirect.com/science/article/abs/pii/0076687987540769

By the way which yeast species and strain are you using? Do you add uracil as supplement in the media? Have you considered the right concentration of 5-FOA? Is your URA3 disruption/excision hapenning correctly?

I think critically analysing these aspects could help you troubleshoot your experiment/study.