Let's start with the fact that some mods can only be charged using micro-USB. These are box mods with built-in lithium-ion polymer batteries. This article is not about them — it will only address mods with standard 18 650 lithium-ion batteries.
The thing is that circuit boards have a very simple algorithm — they don't take into account battery overcharging and, as a result, charge till the cows come home. Which is harmful: overcharging lowers both the capacity and lifetime of your battery.
Also there is a small, really minuscule chance of a mod failing when charging. The first versions of the RX200 used to be infamous for this: history remembers stories of how owners charged their mods in cooking pots to get out of harm's way. However, these days this is extremely rare, and not a reason to panic. Just keep it in mind. Besides, we must emphasize that you mustn't vape during charging — this greatly increases the fire hazard. And we absolutely discourage you from dropping your mod when charging it.
Based on all of the above, we recommend getting a separate charger — for example, a Nitecore or an Efest. The Efest charger is smarter because it allows the user to distribute voltage (in order to charge some batteries faster than others), however the Nitecore can charge regular AA batteries — from your camera, for example. They cost as much as a couple of batteries and serve you for many years.
If you still decide to charge your mod via micro-USB, then make sure to remove it in time. Otherwise, the voltage will rise above 4.2 volts, which, once again, is harmful. Don't leave the mod charging overnight, don't vape while charging — this way you can reduce the fire hazard and prolong your batteries' life expectancy.