For the time being, you should consider changing the appropriate data settings in your phone so at least it doesn't exceed the cap for this period or subsequent ones (these are for Android Marshmallow - if you have another OS, the location of these settings could be somewhere else / worded differently):
Settings > Data traffic management > Traffic reminder settings > Monthly data limit > manually enter your package's limit, or 3.99Gb to be even safer
Settings > Data traffic management > Traffic reminder settings > When over monthly limit > select 'Disable mobile data'
Then I would call Customer Services on 789 from your Virgin mobile to get to the bottom of what may be happening.
It was my mistake. On the My Account app it looked like I'd used 3GB but after looking into my account through the website I've realised it's basically 1GB used and 3GB remaining, not the other way round.