Landing the rocket's three boosters, which have on-board navigation systems, is crucial to SpaceX's reusability strategy, which allows lower launch costs.
The Falcon Heavy lifted off from Florida's Kennedy Space Center, the second launch for the biggest rocket in use today. Two side booster rockets flew back and landed at Cape Canaveral. The middle booster landed successfully on a barge in the Atlantic Ocean, but then experienced problems due to rough seas.
At first, the company acknowledged the core booster hadn't remained upright on the barge, called "Of Course I Still Love You" or OCISLY, because of swells in the ocean up to 10 feet. But it wasn't clear what happened.
On Tuesday, Musk tweeted his response to a question about the middle booster: "Engines seem ok, pending inspection." That indicated the company still had the booster and had looked at it briefly.
More speculation from Twitter users followed, including several questions about whether the booster had fallen over on the barge or into the ocean. Musk didn't answer that immediately, but he did explain why the booster fell over.
"The attachment fixtures are different from standard F9 & they weren't ready in time," he tweeted.
That refers to devices on the barge, on the booster, or both, which SpaceX uses to secure a recovered Falcon 9 booster so it doesn't topple over when rocked by waves.
SpaceX uses Falcon 9's much more frequently than Falcon Heavy. The boosters for the Heavy are slightly modified Falcon 9 boosters.
Musk also tweeted earlier that both halves of the nose cone, called fairings, had been recovered at sea and would be used for SpaceX's launch of its own Starlink satellites later this year.
In response to a question on Twitter, he confirmed that the fairings have their own electrical systems, nitrogen thrusters and parachutes, if needed.
SpaceX hadn't accomplished landing the middle booster on the barge with the maiden Falcon Heavy launch in February 2018, so the successful landing this time was still a milestone regardless of what happened at sea.
A statement from SpaceX spokesman Jim Gleeson indicated safety of SpaceX employees at sea was ultimately the deciding factor that prevented recovery of the entire booster.
Another Falcon Heavy launch is expected to carry dozens of military and scientific research satellites into space in June for the U.S. Air Force.
The April 11 launch deployed the ArabSat 6A communications satellite for a Saudi Arabian company.