Incompatibility issues between FOSS (free or open source software) copyleft licences may be resolved through a special agreement with the holder of the proprietary rights to the component to be incorporated in the software. This will require contacting the community responsible for the component. There is a good chance that a special exemption will be granted. In some cases the incompatibility is even resolved by an exemption clause within the component's licence.
As a recent example, the “Taríqa” crisis management software (distributed from OSOR under the EUPL licence by the European Commission – General direction external relations – RELEX), includes the widely used MySQL client libraries (drivers or connectors). These components are typically licensed pursuant to the GPL's (version 2 in this case) which are incompatible with other copyleft licences. In some cases, their integration in the source code of other software may cause the creation of a derivative work to be subject to the GPL.
However, the MySQL licensor (Oracle) maintains a so called “FOSS exception list” which permits distribution of these “derivatives” under the terms of another free or open source licence.
Oracle kindly included the EUPL in its FOSS exception list, exempting from legal compatibility issues the distribution under the EUPL of works including the MySQL client libraries.
FOSS exception lists greatly facilitate the integration of combined FOSS works, by removing the care (and complexity, as the question is unclear in European copyright law) to clarify how far the work is a derivative or a simple combination or aggregation.
If you encounter such issues for integrating other components, please contact the OSOR team, which will support as far as possible.
More information: the MySQL FOSS exception list