Your question would be better answerable if you posted the schematic of your circuit and showed where did you probe your circuit. Anyway, some general considerations can be done.
Continuity testers may work in a couple of different ways, but they usually act as current sources of smallish value (about a mA or less), and check the voltage across the probes (the displayed value may be that voltage, or it may be a reading in ohms).
The beeper is activated only if the voltage is low enough to be considered a short-circuit (i.e. the resistance is lower than some predetermined minimum, say 10Ω or 1Ω, depending on the instruments).
If there are components placed across your output trace and ground, or (more generally) if there is a path in your board made of components that leads from the output trace to ground, the continuity tester may give some reading.
Bottom line: yes, capacitors can give raise to a reading on a continuity tester. If they have small capacitance, and there are no other resistive paths between the probed points, you should see the reading getting higher (in ohms) while the injected current slowly charges the caps. If the capacitors are huge (hundreds of μF bypass caps, for example) you might not notice the increasing reading unless you wait a long time, especially if the injected current is very low.