Is it because I used a poor cut of meat? Did I not cook it fast enough? Should I have removed it from the heat sooner? Is my cut too thick? Is my temperature probe too conservative?
This question is a little vague, but probably your temperature probe is lying to you, or you're not accounting for resting your meat. I would suggest a legit thermometer rather than one that gives you hints about the meat -- you'll have more control over the final product.
Remember that on resting your beef will rise roughly 10F in the middle as the heat distributes. So, if you pull the beef out at 160F, it will be well done by the time you eat it.
If you want Medium Rare, pull it out at 135F.
There are a few things going on here. First, when I test meat without using a thermometer (as most cooks in an industrial/restaurant kitchen do) I use a neat technique that is available to anyone with hands. With your non-dominant hand, touch your thumb meat (the inner thumb, where it meets your hand). This approximates rare. Then touch your index finger to the tip of your thumb (dominant hand). This can approximate medium rare. Then do the same with your middle finger, medium, ring finger well, and pinky, super well.
Actually, most cooks in a restaurant just get used to what the meat feels like since they cook so many steaks.
Now to your question. Certain cuts will feel different when cooked at different temps. Also, certain cuts will look more cooked in the middle and still be tender (feeling like rare - e.g., fillet). So if this is going on, I would just cook the steak until you like it (but remember to let it rest).
In my kitchen, we have several meat thermometers, so your problem can be remedied by testing with different thermometers. I recommend every kitchen have at least two, and probably three. Troubleshooting meat is multi-pronged and learning how to not rely on a thermometer can help a great deal.
I run into this problem when the probe is placed wrong. The tip should be in the center of the thickest part of the meat, not too close to any bones or large fat chunks.
If ti is too far off center, then the thermometer will read done when the deepest part of the meat still has to cook some more.