The Wire library and an ATTiny88 MCU
My issue has ultimately come from some memory differences between the ATTiny88 and the ATMega88 - the latter has twice as much SRAM - 1 kB. There normally have not been any warnings on this running out of RAM issue except for once - can't recall how but Arduino IDE did warn. 

However, until I got to the bottom of it there have been some digging that had to be done. Like getting used to the programmer either working as expected, or erroring and failing, or erroring and not failing. Then there are the, sometimes changing, folders into which Arduino IDE outputs its files. Also there are non-working board configurations causing the used Wire libraries to issue read and write requests followed by just a NAK. Oh, and not to forget about the messed up signals - turns out they weren't messed up, just the logic analyzer was.