The latest standard method for pesticides in food and feed (EN 15662:2018) is now generally used in control laboratories. However, routine analyses of the combination of hundreds of compounds and food matrices highlighted that false positive identification of pesticides in particular food matrices does occur. The aim of the study was to show relevant precedents when thorough investigation was necessary to make a decision on possibly compliant/non-compliant samples. Examples include the pesticide/commodity combination of atrazine-desethyl in date seed coffee, mepanipyrim in parsley root, myclobutanil in white peppercorn, primisulfuron-methyl in herb extract, propham in elderberry, quinoclamine in fennel and tebufenpyrad in dried ginger. These examples, which were presented for the first time, indicated that the identification criteria for some pesticides in certain food matrices, according to the SANTE/11312/2021 guideline, might fail: the general criteria as stable retention time and ion ratio could lead to an incorrect qualification of pesticides. Standard addition was useful not only in compensating for the background during mass spectrometric detection under the confirmatory analysis, but also in the identification process when negligible retention time difference was observed between the analytes and the interfering matrix compounds.