Yes, your immersion chiller may be giving you higher bitterness than calculated by your brewing software, but not much. The isomerisation of alpha acids (the process which gives bitterness to your beer) drops off very quickly as the temperature is reduced from boiling. At 90 degrees you are only getting about 43% of the normal isomerisation and at 70 degrees you are only getting about 7%.
The process I use is as soon as time is up, I start running water through the immersion chiller whilst agitating the wort slightly until it is down to 70-75 degrees. This takes me about 3 minutes and as you now know, you aren't really getting any significant isomerisation from then on. I actually remove the immersion chiller then, and whirlpool it for 15 minutes then use a plate chiller. Above 70ish degrees you are still pretty safe in terms infection risk as the wort is still quite hot. From the sounds of it, you use your immersion chiller for the whole process so I wouldn't be too worried about any extra IBU's coming from the process you are using. It'd be 1 or 2 IBU's at most, depending on the quantity, amount and AA% of your late hops.
Where I have screwed up in the past though, is switching the flame off, and then whirlpooling for 15 minutes prior to chilling the wort. This resulted in some quite over bittered beers. I now always immersion chill immediately no matter what my recipe is. It ensures consistency and a reproducible beer. Once again though, if you are immersion chilling for the whole process, you'd be whirlpooling after chilling your wort, so the above shouldn't really apply to you. It gives you some understanding on what is happening though.
The other thing you may be experiencing is astringency and I also know this through my own issues. Astringency can lead you to think a beer is too bitter when in fact it isn't. Bitterness and astringency are 2 different things but can be confused as 1 until you know the difference. I find astringency to give a long harsh 'bitterness' which I find is like steeping a green tea bag for a long time, or sucking on a tea bag. Mouth puckering is another term used often.
Hope that helps.
Astringency had crossed my mind but I didn't know about whirl pooling the wort to early.
I fly? sparge with 8ish litres of 76C water through the bag on an oven rack top of pot, just trickle. Can this be over sparging? How do you over sparge?
I plan to get a bigger pot because at 30lts I cant do full vol boils and top up with boiling water during the boil. No tap on bot.