If a specimen of rocks are found through out earth entirely of natural minerals but are different minutely from another in size and shape but look to be manufactured by intelligence.
Never underestimate the power of nature! Particularly when dealing with rocks and minerals. I know - I'm a scientist whose job is to make this stuff in a lab. Some natural rocks and minerals are extremely difficult to make.
How science identifies rocks?
It's also pretty easy to distinguish natural specimens from artificial ones. We scientists don't just look at rocks, we use a bunch of multi-million-dollar instrumentation to study them. When using those instruments distinguishing natural from artificial samples becomes as easy as distinguishing an elephant from a mouse.
Your question also asks specifically about the ‘Moqui marbles’ of the Navajo Sandstone:
If Earth only had them would science say they are ancient artifacts from a past civilization?
The answer here is, again, a firm no. This is easy to check because, of course, the ‘Moqui marbles’ had been observed long before Opportunity landed on Mars in 2004, and at that time scientists did not regard them as ancient artifacts from a past civilization. For example, Chan et al. (2000) described them like this:
Small concretions of secondary iron oxide deposits are exclusively hematite-cemented sandstone. These concretions form all kinds of shapes from millimeters to centimeters in diameter, and cut across primary bedding structure. Some concretions are solid spherical balls around unknown nuclei; others are spherical rinds with plain red-stained, host rock interiors (lacking black-colored hematite cement on the inside). Concretions also exhibit forms that appear to have coalesced or joined (similar to two glued marbles), or exhibit a variety of other odd shapes (buttons, disks, irregular knobby forms to spiked-looking balls).
As you see, the authors identify these objects as concretions. (Also note that, although you claim that they're only "minutely" different in size and shape, the description here mentions a great deal of variation in both those properties.) Concretion is an extensively studied geological phenomenon which occurs across the globe. There’s no need to invoke an ‘intelligent manufacturer’ to explain it, whether or not concretions are found on other planets.