The most common problems on the layout that will impact your DCC system are electrical short circuits.
If you find that you cannot get the Track Status light on your command station to come up, or there are numerous beeps from the booster, then disconnect one of the Rails from the booster and the problem should be apparent.
There is an electrical short in your layout wiring.
The quarter test is the BEST diagnostic tool that you have!
With your DCC system up and the Track Status ON, create a short circuit across the rails of the layout every six feet or so by placing the quarter over both rails and the booster should shut down and beep.
If the booster does not beep and shut down, then you have a wiring problem that must be addressed.
Your system manual covers this in the Track Wiring Considerations section.
Gaps, as in rail gaps, are NOT permanent!
They will close up,due to temperature and humidity changes, and cause all kinds of misery.
Many modelers use plastic rail joiners that have a short nub of plastic to keep the insulated rails from accidentally coming together.
Those that cut gaps in their rails for insulation fill this gap with thin plastic and then file it to match the shape of the rails.
Locomotives and cars sitting on turnouts and across gaps have caused more gray hair than kids.
Polarity mismatches between power districts are usually cleared by swapping Rail A with Rail B on one of the boosters.
One way to check this is to select Address 00 and set the throttle to midway.
Check the Command Station and Boosters; the Track Status light for each should show the same color indication.
If they do not, swap the Ral A and Rail B connections of those Booster that are not in phase with the rest of the system.
Track, turnouts, crossovers, wheel sets, etc., must be checked with a Standard Gauge.
The NMRA has a gauge for each scale.
A quick way to identify track problems is to run an analog locomotive around the layout.
Any problem that the locomotive has is most likely caused by the track.