First, let's note that there may be two or three somewhat different versions of that story. Quoting the ISFDB:
The story was serialized in February and March 1950 as To the Stars and first published in book form in 1954 as Return to Tomorrow and then reprinted in 2004 as To the Stars.
I suppose the 1954 book was an expanded version of the 1950 serial. I have no idea if the text of the 2004 book (the one you read, I presume) is from the 1950 serial or the 1954 book or contains further revisions. Unfortunately I don't have either of the books on hand. This answer is based on the 1950 serial, which is available at the Internet Archive, in the February 1950 and March 1950 issues of Astounding Science Fiction. Maybe some revisions in the book you read invalidate my answer, though I'm inclined to doubt that. All quotations below are from the February 1950 ASF, page references and links provided so you can view them in context.
By the way, I would also like to mention that, while L. Ron Hubbard was a good storyteller, a master of pulp fiction, and a spectacularly successful "artist" of a sort, his yarns were not especially noted for their scientific accuracy, so you should not take his math and physics too seriously. For instance, he seems to think that, if you're driving a spaceship at just under the speed of light, you'd better keep a close eye on the speedometer, or you might accidentally go over the speed limit with catastrophic results. The pilot has a gong to warn him if he gets too close.
p. 35, column 2 — p. 36, column 1:
The gong rang three times and then three times again.
Let her go. Let her edge on up to Constant. Let her flash on through zero time and explode to pure energy or let her hang as one ship had at the exact speed of light and hang there forever, impervious, unmoving, her people statues within her, locked, protected and condemned to eternity by zero time.
The answer to your question is that, at least in the original serial, Alan Corday's first voyage on the Hound of Heaven aka the Flea Circus was not a simple round trip to Alpha Centauri, and in fact the error seems to be in the other direction; with stops at Betelgeuse and "Other Ports of Call", he should have been gone for much longer than 60 years. Here the author states correctly that a round trip to Alpha Centauri would take less than 10 years Earth time:
Outward bound on the long passage, outward bound to the stars. He did not know the speed of this pariah nor how close it would come to light. If it was as slow as ninety-four percent it still meant that for every moment ticked by the clocks of the Hound of Heaven, hundreds passed on Earth. If the Hound spent six weeks in a round trip to Alpha Centauri, nine years would pass on Earth.
"As mass approaches the speed of light, time approaches zero." It was his sentence. A cold equation, a dispassionate mathematics, but it was Alan Corday's sentence to forever.
The run to Alpha Centauri would be the shortest trip they could make.
How old would be his people when he saw them next? How old?
Here's what it said on the paper that Alan Corday was tricked into signing.
And he looked down and saw his name on the articles. "The Hound of Heaven. Outward Bound for Alpha Centauri, Betelguese [sic] and Other Ports of Call." He went white and lunged back. But Gow-eater and his friend still had him.
Only one landing is described in the story, on a planet called Johnny's Landing (star unnamed as far as I know), and this seems to be the last stop before the return to Earth.
P.S. The quotation
"The Hound of Heaven. Outward Bound for Alpha Centauri, Betelgeuse and Other Ports of Call."
also appears in a Google Books copy of the 2004 edition, with nothing changed from 1950 except for correcting the misspelling of Betelgeuse. So thdere's your in-story explanation: they did not just fly from Earth to Alpha Centauri and back.