It's mainly because of my OCD, and so that I know I didn't lose a marker. However, you can use a #1 marker in a #2 slot to signify that you're upgrading a level 1 spell to level 2 to gain extra effects. This requires that you know you're going to use an upgraded spell slot ahead of time, however.
For example (taken from a D&D 5e forum post):
When you cast a spell using a slot of a higher level than the spell — for example, casting shatter (a second-level spell) using a fifth-level slot — the spell may have increased effects. Shatter does extra damage when cast using a slot higher than second level. Other spells, such as comprehend languages have the same effects regardless of the spell slot used to cast them