I do simulations by trade, so forgive me if this is more technical than you intended. I will have to massage some of the details to get closer to what actually happens in simulations to cause artifacts like the ones you seek.
First off, we have to start with an assumption: the universe is supposed to be modeled as a set of Ordinary Differential Equations (ODE). The current models of the universe are all based on ODEs. We have to assume that velocity is a measure of the rate of change in position. So we're detecting differences between what the universe actually is and what could be represented as ODEs. If the universe is supposed to be something other than ODEs, then the actual answer of what we detect is completely dependent on what the laws of the universe actually are. If my universe consists of "Use the known laws of physics until Jan 1, 2020, then break all the laws and summon a dragon into the middle of Washington DC," then that's probably the artifact we'd notice!
Next, we have to point out that "frame-rate based" is only part of the problem. One of the nice things about ODEs is that you can solve them perfectly given one frame: the initial state. This means that our frame rate could be as low as 1/113 billion years ($10^{-19} Hz$) without generating any artifacts. That number, of course, is the current predicted lifespan of the universe, from big bang to heat death. If you want a different estimated lifespan number, you get a different minimum frame rate, but the numbers are equally broken. It's not just the frame rate that matters.
To see the artifacts we need to start taking shortcuts. The first shortcut we take is to say that we don't process everything. We observe convenient symmetries, and we take it. If I'm simulating a pingpong ball flying through the air, I typically don't model every atom and the inter-molecular forces that hold its plastic shell together. I model it as a "rigid body," with a position, velocity, and a rigid shape.
It's when we take these shortcuts that we run into frame-rate issues. If my rigid body assumption on the pingpong ball is not reasonable, then I generate a poor model. For example, during the impact between a pingpong ball and a paddle, the ball deforms quite a bit. I need to remember to model this period differently, with more expensive physics.
The most common frame-rate issues are the ones mentioned in others: interactions between two solid bodies that don't follow the laws of physics. This happens because the simulation starts at a frame where one of these simplifications is valid, but during the integrated path of the universe, those assumptions broke down. A pingpong ball can be modeled as a rigid body, until you have to model the eletrostatic interactions between it and the paddle which deform it during a hit. If you use these assumptions when you shouldn't, you get artifacts. You get fast moving objects that pass through eachother. You get solid objects that stick together. Stuff like that.
This issue doesn't happen in conservative simulations. Conservative simulations will do some sort of look-ahead process to see whether it can prove the simplifications will still be valid. If so, it does it the easy way. If it can't prove it, it does it the hard way, even if it turns out that those simplifications would have worked for the actual path (it's hard to find 100% whether the simplifications hold, but finding the 99% case and being conservative 1% of the time is easy). For example, your simulation might virtually "expand" every object in all directions by its velocity + max-acceleration * frame-period, and then look for collisions. If there's a collision in that expanded world, then its possible that one will happen in the real world. If there's no collision, then it's easy to prove that no collision would occur in the real world as well. This approach is very fast, computationally, and will let you avoid these frame-rate artifacts. We wouldn't observe anything as being wrong.
Now we typically don't solve these ODEs directly. We do what is called "numeric integration," which is an approximation tool. Some numeric integration approaches have artifacts that we can detect. For example, if you have a bias in your equations, you may develop what is called energy-drift. When this happens, your equations predict that energy will be conserved, but the approximations actually don't perfectly conserve it. This can accumulate over time and be detected.
Of course, we have solutions for that as well. This energy drift is easily accounted for using Hammiltonian mechanics, which admit a particular class of numeric integrators which are sympletic. These integrators do not have energy drift, because they only integrate along paths that conserve energy. If the universe used one of them, we'd never see it.
Now with all of this, we leave open the question: why? Why does the universe exist with a frame rate. If it exists because an intelligent species created a simulation,
we have to ask whether they are designing their simulation to fool us within the simulation. If so, it's much harder to notice artifacts because someone is actively trying to prevent you from noticing. If I'm simulation a machine vision system for a robot, there's a whole host of artifacts that I don't actually care about because I know the algorithms the development team are putting together happen to not see those artifacts. If they add an algorithm that does see it, I'll have to change my simulation to model the physics more accurately.
For example, if there is some fixed number of frames per second, you'll see harmonics form in the small number of multiples of frames per second. You'll see things like aliasing if the algorithm is simple. However, modern simulations have something called adaptive frame rates available. If the situation gets complicated, you just decrease your frame period to improve the resolution of your answer. You can always do this unless the simulation has to run in real-time (in some true time sense). In that case, you'd look out for the out-of-simulation entities which don't seem to obey the laws of physics.
So in the end, there's lots of open questions, but the real answer is that you might be able to see the frame-rate in some trivial way, or it may be intentionally obscured from you so it can never be seen. The story is yours, design it as you see fit.