Hello @Aioriaa,
The pinch berries have been tested and they work at 25% or under of the total HP, as intended. What happened in your case specifically is that your Kommo-o isn't exactly at 25% after using Substitute and Belly Drum. This is due to its total HP stat not being divisible by 4, so when using Substitute, you lose just under 25%. The maths:
286*0.25 = 71.5 [PRO rounds every decimal number down, for example 99.99 would still be 99 and not 100] = 71 (HP deducted from using Substitute)
286*0.5 = 143 (HP deducted from using Belly Drum)
286-71-143 = 72 (HP after a Substitute and Belly Drum, as shown in your screenshot)
72*100/286 = ~25.17% (rounding doesn't apply to percentages)
The easiest solution is to either lose or gain 2 HP, making the total HP divisible by 4. Adding 8 EVs in HP should do the trick.
If anything wasn't clear enough or you have additional questions, please do let me know. Have a nice day!