I guess is proposital not a bug, but I disagree, I prefer that mod doesn't use companies slots for each Stock Exchanges existent at Country

Are you talking about the country modifier "has financial center" which adds a certain number of company emplacements based on the number of financial center levels?

If so, you should know that it can take at least a month for the modifier to update with the new number of financial center levels. In addition, the base rate also affects this value. For a base rate of 1%, the total number of companies = number of financial center levels. Then it decreases to 10%, where the number of additional companies is 0.