It's not a bug per se... It's always been like if you have mixed medals, it will always choose the highest level medals first, then if it's not enough it will add the lower tier medals.

That's why if you have mixed medals, always check your great hall often, and use the upgrade immediately after your highest medal is enough

For example you want to upgrade level 4 GH bonus, it needs 400 silver. You have 250 silver, and you are now at Gold tier and collecting gold medals, so you need only 75 gold medals. You have to immediately upgrade that lvl 4 GH bonus once you have gain 75 gold, the silver medals used in the upgrade will be reduced as you gain more and more gold medals.

For example if you gain 100 gold medals, the medals used for that lvl 4 GH upgrade will be 100 gold + 200 silver, meaning you will have extra 50 unused silver medal.

I agree that it should be counted with lowest medals first, but currently it is not a bug, it is how they count it.

Edit: so in your case, that you now have 400 gold, it will always force you to either use 400 silver or 200 gold, I am sorry but currently the only way to do it is either to go back down to silver and gain 100 more silver medals OR use the gold medals, and use the silver medals on other upgrades (when you have not enough gold medals)

For addition:

I honestly think that going back down to silver is inefficient and would cost you more time and arena coins.

I would assume that you still have many silver tier upgrade that you haven't done.

So my suggestion

1. Use the 200 gold for that lvl 4 upgrade, and use 200 more gold on other lvl 4 upgrade and collect exactly 50 more gold for another lvl 4 upgrade

OR 

2. Use the 200 gold for that lvl 4 upgrade, use 200 gold + 100 silver for lvl 5 of that GH bonus, collect 200 more gold to use it with the remaining 200 silver for lvl 6 upgrade of that GH bonus.

For all of those suggestion please be mindful of your current gold medals so you don't exceed the minimum amount of the gold medals needed.