Q1 is connected upside down with S and D pins transposed. This causes LED1 to be permanently conducting through what is therefore the forward biased body diode of Q1. Without a photo of your PCB it is not certain but it would seem most likely that you have a dry (open circuit) solder joint at one end of SCAP, removing it from the circuit so allowing Q2 to turn on immediately. An less likely alternative is that you have accidentally fitted a PNP transistor in place of the NPN for Q2. Or you have shorted out R1. R4, R5 and the diode drop across the base-emitter junction of Q3 create a potential divider that holds the voltage across C1 and therefore the input to U4, the Schmitt trigger inverter, below the upper (logic 1) trip threshold. Therefore the output of U4 is permanently stuck at logic 1 so Q3 is always on, illuminating LED3. If you want LED3 to flash then connect R5 to the output of U4, not the input.

"An less likely alternative is that you have accidentally fitted a PNP transistor in place of the NPN for Q2." Ignore that one. With a 3.3V supply at both the collector and base circuits, replacing Q2 with a PNP would not cause the LED to illuminate.