SysTick timer is part of the Cortex M0 (PSoC 4) devices. The timer is a down counter with a 24-bit reload/tick value that is clocked by the System clock (or LF clock for the PSoC 4100 BLE and PSoC 4200 BLE devices). The timer has the capability to generate an interrupt when the set number of ticks expires and the counter is reloaded. This interrupt can be used as a wakeup source when system is in Sleep mode but SysTick interrupt cannot act as a wakeup source when the system is in Deep Sleep mode.
Can you please share me the project so we can see what actually the issue is.
Are you using debugger while the device in deep sleep mode?
Also, did you try measuring the current to confirm if the device is in deep sleep mode?