Some icons, i think its the ones that display both a buff and the cooldown, gets the modRate set to 0.001
I only found a bandaid fix to it i hope this will point you towards the correct place to fix it.

\Interface\AddOns\OmniCC\core\timer.lua
Row 50 that says "local modRate = cooldown._occ_modRate"
Under that row paste "if modRate < 0.01 then modRate = 1 end"
Save and the time is now displayed correctly. (if the modRate is 0.001 and not something like 0.0013)

Edit: This most heavily affects OmniCD but i've also seen some stuff in WeakAuras get a cooldown of 1 day etc.

Okey, In cooldown.lua, the function Cooldown:Refresh(force), you use both GetCooldownTimes() and GetCooldownDisplayDuration() which the wiki says are both in ms, afterwards you change 2 out of 3 returned variables to sec but then use the unchanged rawDuration to calculate the modRate which causes the issue.

My fix so far is after checking rawDuration > 0 on row 331 simply do rawDuration = rawDuration / 1000