I normally don't care that a PC uses magic items to deal with encounters, but I have a player whose PCs are notorious for using rods of force (Magic Item Compendium 174). His PCs find or buy multiple rods and use them instead of their innate abilities to overcome challenges.
Is it unfair to remove this item from the game? I don't want to, but, at the same time, the player's made previous game sessions too easy using this item, ruining the challenge.
Yes, of course, removing a problematic element from the game is one of the reasons to have a DM in the first place.
But I have a hard time seeing how rod of force is that item. They’re extremely expensive (worth almost everything an 11th-level character owns, and not being realistically affordable until 15th or 16th level—and that’s just for one!), can only be used five times per day, and it functions as either a mediocre weapon, a mediocre blast attack, or wall of force, which is almost-certainly the best way to use it but I have hard time seeing how that could ruin a game. They’re fairly decent I suppose, with that flexibility, but I just don’t see how they end up being game-breaking.
For rod of force to cause so much trouble, I have to imagine that this character has vastly more wealth than the books would otherwise suggest. With that much wealth, they could be getting far more dangerous things than the rod of force. I suggest your review the wealth by level guidelines in the Dungeon Master’s Guide, unless you’re playing in the 15th+ level range—at which point, I would suggest your encounters need to be tougher if the rod of force is causing considerable problems for the players’ encounters. On a personal note, I generally feel that the game breaks apart on its own somewhere around 15th level, without any need for particular player shenanigans. I would thus suggest avoiding games that go so high, the system doesn’t work well when you do.
Perhaps an alternative solution is to use supply and demand. You can role-play the PC's attempt to buy the rods, and if the PC can't find any (or there is only one in the area available and the mage who owns it does not want to sell it), the PC will not be able to get one. Just because an item has a price in a rulebook does not mean the item is available, especially a magic item. And (on a side note) you can make it hard / dangerous to get to the rod (using up some / most of the charges getting back with it).
You can also have the rod be under-charged - how does the PC know how many charges are on the rod? After the PC buys 3 rods for full price, each with 2 charges, they will think twice about buying a fourth..
