This is usually the result of overlapping atoms in your initial configuration, but it’s impossible to say without more information. The general strategies are, apart from nve/limit, to do an actual minimisation (minimize command), or to use something like the soft pair style to remove the overlaps.
Or identify the flaw in the starting geometry and remove it.
could you please resend the original message, since apparently it has gone missing at some point.
Re geometry I should add that the problem is related to arbitrary hydrogens in a metal lattice, which I would like to keep there if possible.
You can't just put atoms anywhere. Just change the tool you use to place them so they cannot be placed too close to some existing atom.
Or use pair style soft with fix adapt on them to unoverlap. See the micelle example. Only keep your lattice immobile.