Were they the same research facilities that were previously on both tiles and was there ever any other type of building on either tile?

When you upgrade you get credit for some portion of all the money (or production) previously spent on that tile. In the case of an upgrade to the same type of building you should get total credit for the cost of the previous building. If it's a different building type then you only get some undefined percentage of the cost of the previous building. AFAIK you do get some credit for all of the buildings previously built on the tile.

Also are you sure that you're upgrading and not just building a new building on top of the old. There can be a subtle difference that's not always noticeable.

For example if you select the tile you wish to "upgrade" and then you double click on the new building then the up arrow appears and then when you buy the building you're paying the upgrade cost. If instead you select the tile and select the new building by clicking on it (not double clicking) and then press buy you're simply buying the building directly and not paying the upgrade cost. In the latter case the up arrow would fail to appear before buying the new building.

Also you need to be a little bit careful about doing this. Sometimes the direct purchase price is cheaper than the upgrade price although this usually seems to apply to the cheaper buildings. For example direct buying a Starport is always cheaper to buy for 156 bc than it is to upgrade over any other type of building (~468 bc).

@Mumblefratz

I'm positive. This was a completely built up tecnological capital. I had auto-upgrade on and the upgrade arrow was there on all my research structures. And yes, I clicked on the tile with the arrow already there. The research structure on the 300% bonus tile simply cost more than the same structure upgrade on all the other non-bonus tiles. I think I might have been getting some credit for the existing structure, but the bonus tile (or something else) was affecting the upgrade cost.

Thanks for the advice about not upgrading to Starports!

I don't understand. How do come up with the 9.5? How does the bc cost relate to production capacity (and/or production bonuses and/or the social/military/research sliders)? How would you factor in changing plantary focus? Can you divide by 9.5 in your head or do you have a calculator handy?

Edit: I just looked at this post and it seemed a little snippy. This is not intentional. I really am just wondering where you're coming from. It seems to me that the cost of a structure or an improvement should be independent of everything except the initial cost in hammers, the remaining cost in hammers and possibly the planet type (including if you have advanced colonization in that planet type) and the planet quality.