This is not necessarily the case. If you can use the desk light USB outlet successfully now, after the charger has appeared to work properly now, then this will prove that it’s not the desk light USB outlet.
My guess as to what happened is that the charger was far too deeply discharged that the battery voltage was below the safety threshold level where the system is allowed to recharge it. So when you tried to plug it in, nothing happened except for the red flashing system error lights.
Hours later after you left it alone, luckily the battery was not completely dead for good, so it was allowed enough time to do some self-recovery, and was able to recover and push its voltage output back to be above the safety threshold level where the system would be allowed to charge it again.
You can find plenty of YouTube videos that show you tricks on how to apply a direct voltage to a dead lithium ion battery (like a Ryobi tool battery, for example) that would otherwise seem to not be able to be charged up anymore, so that it would get “revived” with the external voltage “jolt” to feed it enough current to bring it back from the dead. Not a full recharge by any mean, just enough to “wake” it up to hold some bare minimum voltage for the charger to recognize that this is not a completed dead battery, but only a fully discharged battery. Then the charger is now allowed to charge the battery once it sees a minimum rechargeable voltage on the battery.
Of course in your case, there’s no access anywhere to apply this trick. The only thing you can do is to leave it alone for a few hours or a day or two and hope that it can recover by itself. Many rechargeable batteries, when fully discharged, as long as they’re not dead completely, might be able to self-recover with time to allow the chemical process to happen inside the battery to rebalance itself back to a small positive charge. As long as this small positive charge is above the safety threshold level, the charger will be allowed to charge it again at that time.
The moral of the story is that don’t keep using the smart charger for more cycles then the spec says it is designed to provide. If you do so, you may run the risk of discharging the battery too deep and next time, you may not be lucky enough to see it recover itself.