I was having some problems in my server since I first run it about 2 days ago that makes some blocks unbreakable. I don’t know if it’s just me but it’s pretty strange.
I don’t know if this is the case for your problem. There is a minecraft spawn protection so that non-op players can’t break blocks in a configured radius around the spawn.
If that could be your problem set
spawn-protection=0 (in server.properties)
I think there might be something similar in the bukkit.yml, spigot.yml or paper.yml which you also have to set to 0 but I am not quite sure and I did’nt find something in my short research.