An en -> fr project with a glossary including two entries, like so:
| Source term | Target term |
|---|---|
| actvity | activité |
| establishment | établissement |
The source text includes the source terms:
Please choose the sector code that best applies to the establishment’s main activity and product.
The translation adheres to the glossary and uses the target terms in it:
Veuillez choisir le code sectoriel qui correspond le mieux a l’activité principale et au produit principal de l’établissement.
No issues flagged, because the translation complies with the validated terminology.
Both glossary entries trigger terminology issues (allegedly because the apostrophe is not recognized as a stemming point).
l'activité
l'établissement

The same issue might happen in other languages with similar orthographic singularities, not tested.
The issue does not reproduce if the translation does not include an elision of the definite article, e.g. .
Veuillez choisir le code sectoriel qui correspond le mieux a notre activité principale et au produit principal de notre établissement.
Test project attached.
Reproduced with version OmegaT-6.1.0_0_7aaa8b806 and earlier.