The most frequent problems found in pipe organs are dead notes and cyphers; the latter are pipes which sound when they should not (See blog, Cyphers).
In the case of dead notes, if we can reproduce the problem from multiple places we can pinpoint that the problem is at the pipe and not in the relay.
This is called triangulation, and it's a helpful skill.
If, for example, we discover a dead note on the low F6 on the Great 8' Concert Flute, and we find that the 16' Bourdon in the Pedal is also dead on tenor F18, and if it's the same stop, same pipe, we've triangulated where the problem is.
It's a good idea to keep a notebook where a record can be kept of issues like this for the organ technician.
By far the simplest of systems for communicating to the technician which note or pipe is the problem is to count keys from low C; in this system middle C is #25 and there is no confusion about which key on the keyboard is intended.
These written notes should be clear and specific; if we write "D is dead," or "D3 is dead," the technician will not know exactly what we mean, where to look, or which stop to check -- but if we write "Swell D27 8' Oboe Horn is dead" there will be no confusion; the problem is middle D on the Swell Oboe Horn 8'.
From the builder's perspective the organ has only sharps; key #4, for example, is low D#, never low Eb (E flat); this system should be used when leaving notes for the technician; vague messages such as "Viole is out" requires the technician to do a fair amount of detective work just to locate the offending pipe, which results in poor time management, delays, and additional expense.
A pipe that worked yesterday or last week and does not speak properly today might also have a foreign object in it, such as flies, boxelder bugs, Lady bugs, or even gum wads, rubber bands, birds, bats, or paper airplanes.
If possible, we try to find the foreign object and remove it, being careful not to bump the tuning slide or scroll; when the pipe cools from our body heat, it will be in tune once again.
Reed pipes are notorious for flying off proper speech from dirt; often the whole rank is affected, and usually the technician will need to clean them.
Cleaning all the pipes from top to bottom should be budgeted at least every 30-40 years.