The second voice we hear in "Back To The Future" (after a radio commercial for Toyota cars) is a TV newsreader describing an alleged theft of some plutonium which was now believed to be a simple clerical error. Then we see Marty's skateboard run into the side of a case containing plutonium. So why was it considered to be a clerical error? Did Doc, at some later point in time, travel back and replace it, or amend the nuclear plant's records? Or was it a different nuclear facility that he stole the plutonium from and this news report was a coincidence?
He could have, but nothing like that is ever shown.
Doc still has the plutonium at the end of the movie - he jumps to the future with it, because the DeLorean still needs that fuel. It's likely he got rid of it once he had the new Mr Fusion as a power source, but it's never brought up where he ditched it.
The news report only indicates that the plutonium was indeed noticed missing, and this is likely when Doc's terrorists stole it. If Doc had returned what was left (presuming he would be able to do so, he's not the stealthiest of people), they still would have been short the pellets he used, and the news report would still have happened. If he altered records, the theft would never have been noticed at all, and there would have been no news report, so still not likely.
The only reason the news would report a clerical error is, in typical fashion, someone attempting to cover up the theft rather than admit there's plutonium loose and no one knows where.
The Doc used some of the plutonium in the various time-travel trips before he got Mr. Fusion, so if he were to replace it, he'd have to replace it with less than was stolen in the first place, so the theft would still have been noticed.
Although it's an interesting possibility. He'd have to have replaced it at a point in time after it was noticed missing, but before the "double-check" (at which point the people in charge would believe it's a clerical error). This would make sense in a way, because if he replaced it the instant it was stolen, he'd have risked running into the Lybians and interfering with their stealing it in the first place. But that's all "Wild Mass Guessing" as the TV Tropers say.
It's more likely that the facility covered up the loss because it's a serious thing to lose plutonium.