Hi Holger,
Well what the error itself means is that the JaCoCo reports contains coverage data for a line that is not found in the corresponding source file. So I would more specifically put the responsibility on the overall Continuous Integration chain: at any point in time it’s important that the coverage reports present locally correspond precisely to the actual source files analyzed locally.
If any slightest mismatch (e.g. source files changed after coverage data was computed) then failing is the only viable strategy, otherwise you run the risk of having totally incorrect data reported and tracked by your team (in that respect, silent failure or incorrect data is worst than any failure at all).