Some applications are not compatible with unionfs (the filesystem which performs the union mount).
For example Vagrant, with its nfs mount and of course the nfs itself.
What to d?
For this kind of applications, I use a 5th ext4-formatted partition for the purpose and mount it where I need (via fstab).
I created it by shrinking the persistence partition and adding a new one by booting with a live operating system – in the image Ubuntu – and using GParted.