When the 100-ton Columbia was ferried back yesterday from Edwards Air Force Base in California to the Kennedy Space Center in Florida, it was two days late, and therein lies the most glaring trouble facing the space shuttle.

The trouble is with "turnaround time," the National Aeronautics and Space Administration's expression for the time it takes to get the space shuttle ready for flight again after it has completed a mission.

The first spacecraft ever built to be reused again and again, the shuttle's future hangs on how quickly it can be readied for its next flight. In short, how brief can the space agency make the space shuttle's turnaround time?

Two days late in leaving California is not a big problem itself but it is symptomatic of a much bigger one. So far, the shuttle has never been on time for its appointments.

It was more than two years late for its first flight, was almost two months late for its second flight, which was just completed, and will be almost two months late for its third and fourth flights. This means the turnaround time between the second and third flights will be between four and five months.

Its fifth flight, the first operational flight after the four-flight test program, is scheduled for next September. Nobody in the space agency thinks the shuttle will make it by then.

"It will take an unusual combination of effort and good luck to make that fifth flight on time," says an official at the Kennedy Space Center where Columbia is flown. "I don't see how we can make it in September."

What worries shuttle managers most right now are the costly delays in getting the shuttle ready for its first two flights. Twice, launch directors have readied the shuttle for flight only to scrub the flight both times in the final minutes of the countdowns.

The two scrubs have cost NASA almost $40 million; the two months the space agency is behind in the shuttle's test flight program will cost it at least $180 million.

The first of the two launch scrubs was called when the shuttle's four on-board computers were found to be fractions of a second out-of-line with each other.

The second scrub was called because the filters that feed lubricating oil to the shuttle's hydraulic system clogged up minutes before takeoff. Incredibly, neither the oil nor the filters had been changed after the first flight.

"The fact that we had a problem with those filters indicates we have to do something different after each flight in the way of maintenance," Shuttle Launch Director George F. Page said after the second scrub.

Whatever new procedures are required will take time, which will add to the turnaround time between future flights. Suppose new troubles show up on the next two test flights the way they have on the first two? Again, any new troubles will result in a longer turnaround time.

Shuttle managers used to talked of a two-week turnaround time between flights for each space shuttle. No longer. The best they now talk of achieving is five weeks and most think an eight-week turnaround time is more realistic. Even an eight-week turnaround schedule will not be met, most shuttle managers say, until sometime in 1984 or 1985 after the shuttle's 25th flight.

"This five- to eight-week turnaround time is the best we'll ever see," Page said. "We'll certainly never see the time when any of the four shuttles we have flying can be turned around to fly again in two weeks. That's out of the question."