Yes, it sounds like the steerer was cut shorter than optimum for three spacers under the stem, but whoever set up the bike thought the stem needed to be lifted that high. No matter if you want to ride on lower bars. Just discard the extra spacer immediately, but be sure to cut the steerer properly if you decide to get rid of all spacers. Once it is too short with no spacers, there is little you can do to fix it. And as recommended above, don't cut until you are sure you like the new position. In case you decide to raise the bar again, you should probably go no higher than two spacers or maybe two of the size you have and one thinner one.