Someone I admire greatly says this about rules of thumb - in another field, but it applies equally well to crosswords.
Regular solvers will be accustomed to replacing "way" with ST or "fifty" with L in their heads without second thought, but sometimes a clue comes along that upsets that convention.
So it is with charge = ION. That isn't even much of a "rule of thumb" – exceptions are abundant!
When is charge in the surface not equal to ION in the solution? Here are a few cases:
1. When "in charge" = IC
Guardian 24714 (Rufus): Commanding Officer in charge set about sergeant major – great! (6)
ET 3220: In charge of an animal, in charge of a country (9)
2. When it means "accuse"
Times 24234: Reportedly, a means to control horse's charge (7)
THC 9548 (Sankalak): Charge that supporter is steeped in drink (6)
3. When it means "control" or "supervision"
New Indian Express 31-Dec-08: One in charge is possibly a German (7)
THC 8898: People in charge of wardrobes and cupboards (8)
2. When it means "payment" or "price"
New Indian Express 07-Jan-09: Anticipate charge for concealing minerals (7)
New Indian Express 19-Nov-07: Soldiers hold deserter without charge (6)
4. When it means electric charge
Guardian 24717 (Araucaria): Store charge here for top performer without one (9)
New Indian Express 9871: It's extremely small and free of charge (7)
Answers? More clues that use CHARGE in another sense not mentioned here? Share them in the comments section.