Do modern airliners have a flaps warning indication? Years ago I was on a flight from San Francisco to Los Angeles, a 737 if I remember rightly, and was sitting just behind the wings and could not help noticing the flaps were partly extended for the whole flight. 

I thought they looked odd out the window but did not bother mentioning it to the cabin crew since I was not sure what I was seeing. However, on landing in LA, the pilot retracted the flaps after using them for landing, and they were then correctly seated. 

I assume the pilot felt something was off, since after landing I could see ground crew wandering around and inspecting the aircraft with puzzled looks on their faces.

I understand that the flap controls are a bit out of the pilots normal sight lines and this got me wondering whether there is instrumentation in the cockpit that alerts the pilot to the fact that the flaps are not fully closed once in normal cruise attitude. Perhaps even an indicator similar to the landing gear lights.
It could have been as you witnessed.

In 2005, a modification package dubbed Quiet Wing was offered for the 737-200 and the 737 Classic (-3/4/500) that would droop the flaps by 4° for all phases of flight.


  [It] decreases drag for cruise, and increases the aerodynamic efficiency of the wing by between 2% and 3%.


The NTSB in 1981 also found that many 727 pilots were doing the same thing in cruise—but manually and unapproved. They would pull a CB to keep the slats on the leading edge of the wing retracted, while the flaps extended to the their first stop.


  Investigators believed that 727 pilots (in general, and this flight specifically) were setting the trailing edge flaps to two degrees during high altitude cruise, while at the same time pulling the circuit breaker for the slats so that they would not activate. This configuration was rumored to result in increased lift with no increase in drag, thus allowing more speed, higher elevation, or decreased fuel consumption. Flaps and Slats were intended to only be deployed at low speeds during take-off or landing.


To answer the title question, yes. Flap position indicators exist, and combined with the electronic speed tape, the maximum speed indicated will be slower.

If the flaps were to be extended at above design speed, an overspeed warning will be triggered as well.