Your description is somewhat patchy (much exposition, little info). However, I suspect you're planting in early spring and saw plants spring up around your feet immediately, but those plants weren't visible later. If that's the case it's somewhere in the borderlands between bug and feature: You've planted late enough to plant, but not late enough for the plants to actually sprout (which can happen a week or two later depending on the plant). Those plants will sprout "for real" when they're due, so you haven't actually lost anything in that case.
It can also be noted that some plants have exactly the same hue as some types of ground during some growth phases, making them effectively invisible during that time, but that's probably a different issue.
And no, it can't be bugs, because they haven't been introduced yet. They'll probably appear together with other calamities such as droughts and rats