Christos, if you have several components that are connected to two wires (or traces) and one of them is shorted, no matter where you test you will get short.
----A1----B1----C1----D1----
----A2----B2----C2----D2----
For example, let's say there's a capacitor (or any other component that's not normally short) between A1 and A2, another capacitor between B1 and B2 and so on.
If there's a short between C1 and C2 and you put the multimeter probes on A1 and A2 your multimeter will say short even though there's no short directly between A1 and A2, because the signal from the multimeter will go A1 to B1 to C1 then pass on to C2 and move to B2 and finally reach A2 ... so your multimeter will say there is a short between A1 and A2 even though there is no direct short.
If you want to truly test one component, you have to pull out at least one of its legs so that the signal from your multimeter won't go through the traces on the pcb through another component that's shorted.
Now if you have a very good multimeter (for example on with 40000 counts or more) that can show very small differences in resistance, you could actually determine where the short is because the actual resistance changes with the distance the electric signal has to go through.
For example, if there's short between C1 and C2, when you put probes on C1 and C2 you would get 0 ohms.
But, if you put the probes on B1 and B2, now the electric signal has to go from B1 to C1, then from C1 to C2, then from C2 to B2, so there's a longer distance. Your multimeter may now show 0.0001 ohms.
If you put probes on A1 and A2, the distance is even longer, so the multimeter may show 0.0003 ohms.
If you see resistance increasing, you know you're moving away from a short.
But again, you need a very good multimeter for that, a cheap 5-10$ (well, often not even <50$ ones) will not be able to help you with something like this.