Add a new property to product attributes (combined/non-combined). When generating (manually or automatically) combinations, only the combinable attributes will be presented
When you have a product with several attributes it may well be that some are combinable, whose combination may form a new SKU with its own inventory, and some non-combinable are more used to add accesories. Example a shirt might have as combinable attributes sleeve size, neck size, color and material and can have other non-combinable such as initials embroidered (text and 2 options for embroidered in chest or cuff ) and cuff links (1 of 3 options which could well be associated products).