Questions like this do touch the nerve of the film's logical consistency.
In our normal, non-inverted timeflow, when you shoot a wall/glass, the resulting hole remains in it indefinitely and only gets worse with time. It will eventually get buried/destroyed after the building gets demolished. The hole will not magically self-heal / disappear.
In Tenet's inverted timeflow the laws of physics are deemed to be all the same. It's just the entropy/time that flows in the opposite direction. So, there should be no reasons to presume that the behaviour of a bullet hole shot by an inverted round would be any different in its timeflow. Like with a normal bullet hole, it should be worsening with its time going forwards (ours backwards), not self-healing.
What that means is that, logically, the hole got formed it its worst/oldest state in the glass right when it was solidifying from liquid silica at the glass factory. Yes it was essentially a factory-made flaw/defect which, for whatever reasons, was ignored by the factory's QA, glass supply chain, the builders and the Freeport vault staff all the way along. Think they all were on Tenet's payroll or whatever.
Like Barbara said to the Protagonist: "Don't try to understand it. Feel it". I don't think Christopher Nolan intended to make it completely logically consistent and making sense. It's just supposed to be a "wow" to impress the majority of viewers who will simply say "Ingenious! Let's go see it again, maybe we'll understand some more".