Are you using the ILO as the Clk_LF? You can check that in the Design Wide Resources > Clocks > Miscellaneous Clocks.
If yes, try to enable the WCO and source it to Clk_LF and see if fixes the problem.
I have seen some issues to use the ILO before in Deep Sleep.
Thank you for your answer.
Yes, I am using ILO as source for CLK_LF. I don't have an external 32 kHz oscillator connected to P0_0 - I use that pin for a high-frequency oscillator instead, so WCO won't work for me.
I can't see why it shouldn't work with ILO.
Could you upload the project here in the community? You could remove any confidential code and just leave the watchdog part.
I tried to reproduce the problem, but I couldn't.