You have quite the interesting story here. One of your strengths is that you have a variety of syntax. Your short, motivic sentences are engaging and effective, and you seem to use them in the correct places. For instance, your motive "He stared at it....It stared back." gave the story a strong beginning and ending.
The story is creative, but I think you can do more. So, Mason really likes coffee, got it. There are aliens lurking about, got it. And, yes, Mason's desire for coffee ultimately proves to be his undoing because the alien happened to be creeping around the coffee shop. But, this incidence is purely coincidental, other than the mysterious lights which spelled the word "Coffee" in the fog. But, why is "coffee" spelled in the fog? Was Mason specifically targeted? If so, why target him? What makes him special? Why do your aliens necessarily have anything to do with coffee? Can you think of a creative connection for that and implement it? A stronger and clearer connection between the two would make the story more engaging and complete.
Okay, now for grammar. I'm going to make some constructive suggestions to you for editing. Buckle up.
"...the bed was empty..." "...the shower was off..." Try and avoid too many "to be" verbs. Usually you can think of better, more fluid verbs which condense your sentences or are more precise. For example: "the bed emptied" or "the shower turned off".
"...Mason was running..." For this, you may simply say "Mason ran." Trust me.
"A fog slightly thicker than the one in his caffeine-lacking mind." This is a sentence fragment. Though I was quite fond of the description and the pun in this, it isn't a complete sentence. Think of a way to combine it with the previous sentence or make it complete. It's all subject, no verb.
"...sounding genuinely startled." The word "sounding" here is redundant. "genuinely startled" or even just "startled" would serve your purposes.
"...working it out in his head..." Grammatically, this is correct. But I think you can use a more precise verb or verb phrase here, like, "mulling it over" or "considering it" or "contemplating it."
"A couple began moving to the door." Try not to have the subjects of your sentences "begin to" or "start to" do anything. Just say, "A couple moved to the door." That sentence is cleaner. Also, the description of the couple moving out of the door really doesn't have any function to your story. It's like a random observation and had nothing to do with the coffee machine breaking down.
"...ran outside, into the fog." No need for a comma there.
"...began trudging...Mason started sprinting." Again, just say "trudged" and "sprinted."
"...was running..." Instead, just say "ran" or "dashed" or "hurried" or something else.
Mason's curling into a ball and waiting for death as a reader I'm a little skeptical about. If he had time to drop from his feet to the ground and curl himself into a position and then wait for impact, he had time to at least try and leap away. Imagine the scenario for a second. True, the only circumstances where someone would not try and leap away would be if they had no time. But if they had no moment to leap away, then they would certainly just be hit while standing on their feet. The moment when someone realizes it's too late, it's too late for them to move at all.
"... a light scraping..." A "scraping" is a verb. You want "scrape", which is a noun, here.
"...breathing hard." There is nothing incorrect about adverbs. However, adverbs are mainly used to supplement weak verbs. Often, you can simply think of a stronger, more descriptive verb in its place. For example, instead of "breathing hard," you could simply say, "heaving."
These are most of the changes I would suggest, and you can figure out the rest using the explanations I've described for you. Now, I know that my review and critiques were rather exhaustive, and I did break your story down piece by piece. My intent is not to discourage you. Rather, I wanted to point out some things that I don't think you had noticed or considered before. Indeed, I do think you have a good story here. I encourage you to keep working on it, continue to edit, and be thoughtful.