Context. The third Gaia data release (DR3) provides a wealth of new data products. The early part of the release, Gaia EDR3, already provided the astrometric and photometric data for nearly two billion sources. The full release now adds improved parameters compared to Gaia DR2 for radial velocities, astrophysical parameters, variability information, light curves, and orbits for Solar System objects. The improvements are in terms of the number of sources, the variety of parameter information, precision, and accuracy. For the first time, Gaia DR3 also provides a sample of spectrophotometry and spectra obtained with the Radial Velocity Spectrometer, binary star solutions, and a characterisation of extragalactic object candidates. Aims. Before the publication of the catalogue, these data have undergone a dedicated transversal validation process. The aim of this paper is to highlight limitations of the data that were found during this process and to provide recommendations for the usage of the catalogue. Methods. The validation was obtained through a statistical analysis of the data, a confirmation of the internal consistency of different products, and a comparison of the values to external data or models. Results. Gaia DR3 is a new major step forward in terms of the number, diversity, precision, and accuracy of the Gaia products. As always in such a large and complex catalogue, however, issues and limitations have also been found. Detailed examples of the scientific quality of the Gaia DR3 release can be found in the accompanying data-processing papers as well as in the performance verification papers. Here we focus only on the caveats that the user should be aware of to scientifically exploit the data.