Sounds like you have the wrong field on your layout.
If you have this relationship:
Maintable::_fkLookUpTableID = LookUpTable::__pkLookUpTableID
For an explanation of the notation that I am using, see the first post of: Common Forum Relationship and Field Notations Explained
and you want to look up data from LookUptable on your Maintable layout...
Make sure that the field where you are entering data is from Maintable, not LookUpTable or you will be modifying the related record.
Sounds like you need to define a field in MainTable, specify the lookedUpValue auto-enter field option to copy a value into it from LookUpTable and then you place this field on your layout in place of the one that you have added from LookUpTable.
Indeed, my field in the MainTable was coming from LookupTable.
Fixed it and all is working as intended, thank you for your advice.