There's a good chance he thought he did.
There's actually an 18.5 minute gap in the tapes, about 3 days after the Watergate break-in. Of course that could have contained anything, including unrelated material. However, even sympathetic administration officials of the time now admit it was probably material that implicated him in the coverup of that break-in.
Now it turned out that other conversations on other tapes still implicated him. Why didn't he get those too? Perhaps he just forgot about them. There're hundreds of hours of conversation on those tapes, and this was back in an analog era when it wasn't a simple matter to compile and analyze data. It could well be that he remembered having such a conversation, he (or someone working for him) found it on the tapes, erased it, and thought they had got it all.
IroniclyIronically, the "smoking gun" tape was found only because that 18.5 minute gap looked so suspicious that Congress subpoenaed more tapes.