The Federal Reserve is putting a wrench in how financial markets should be working by continuing to keep interest rates so low, David Darst, senior advisor at Morgan Stanley Wealth Management, said Monday.

"We're in very irrational times," he told CNBC's "Squawk Box" in an interview. "Things don't work the way they should."

Darst said forget the debate over whether the Fed will hike rates in June or September of this year. Morgan Stanley's chief U.S. economist, Ellen Zentner, sees the central bank waiting until March of 2016.

The Fed will then be behind the curve, Darst said, with policymakers possibly raising rates eight times next year. "And that could upset the market."

Read MoreThis is when to worry about the US market: Tom Lee

The much-weaker-than-expected March employment report, released when the stock market was closed for the Good Friday holiday, raised questions about economic growth, said JPMorgan's chief economist, Bruce Kasman.

Bucking a recent trend, nonfarm payrolls only grew by 126,000 last month, the worst since December 2013, though the jobless rate remained unchanged at 5.5 percent.

"The idea that the economy is going to do better in the second quarter is pretty clear on a number of fronts," with longer-term signs of labor market tightening and wages turning around, he argued, but improving growth won't happen quickly enough for the Fed to feel comfortable increasing rates in June.

Kasman expects a move by the central bank in September. "There's concern about if they go too early and have to reverse. That's something they really don't want to do."

"I don't think the Fed will take that step before they're ready to do somewhere between 100 to 200 basis points of tightening," he continued.

But the real question for the market will be how much rates go up in the next two to three years, Kasman said, an idea that Darst also underscored.