Battery Charging Operation
A battery is a collection of cells. A cell has a voltage defined by the chemistry. For example, all alkaline cells have a voltage around 1.6V. I don't think there are any cells that produce 12V, as you say in your question. You mean battery.

The current is the same everywhere in a series circuit. Charge is conserved, and unless you have some very high voltages, you can't get it to fly off the wires or suck it in from your surroundings. So if you have a series circuit, and you put some charge in, exactly that much must come out the other end. Where else would it go?

Consequently, if you charge batteries in series, they will each receive exactly the same charging current. If they are all exactly identical, and were all exactly as much discharged at the start, then they will all charge equally.

The issue is that real batteries aren't exactly identical. Some chemistries, like lead acid, can handle a small charging current even when fully charged: the charging current then just flows them harmlessly. Thus if one battery charges first, no big deal. It will pass current and the others will continue to charge.

Other chemistries, like lithium batteries, tend to explode if overcharged. Since it's difficult to guarantee that each of the batteries are exactly identical, it's hard to predict which will be done charging first, and since the current must be the same in each battery because they are in series, it's difficult to charge lithium batteries in series.