All is possible in the realm of rat-bastardy!
Question is how much of a rat-bastard are you?
Now obviously these things couldn't happen if the clone was under the influence of a temporal stasis because of the wording that basically put them outside time until the spell ends. If you were using another spell, say the Graceful Repose that was mentioned earlier, there's nothing in that spell description to specifically protect an un-awakened clone. So it would be case-by-case.
An un-awakened clone is not strictly speaking alive(but also not dead it merely lacks a soul). It has all the same types, subtypes as the sample it was made from identical characteristics. And it is completely helpless. So yes I can see some of these conditions being inflicted secretly or otherwise while the clone is inert but there'd better be some backstory set up that justifies it or it'll just make people aggravated.
On the other hand, how bastardly, I wish I'd thought of something like it.
The werebadger carefully eased out of the tunnel carved by a pressing root into the stone room. Already he liked what he could smell in the darkened space. The sharp tang of oil preserved weapons and dull metallic taste of gold coins. A body rested off the ground on an elevated bier perfectly preserved by magic. Not bothering to shift forms he used the gleaming shield propped up against it to reach the surface and smelt, tasted. Just a few bites from the soft flesh of the calves, no something was wrong about it. Distasteful, the body was not alive no but neither was it dead and the soft human meat tasted of fell magics best to avoid. He left the not-corpse to its rest and resumed a human form, so much here to take and from the inside the door wasn't even locked.
Later, perhaps but a few months, perhaps decades passed unknown and something happened. The body breathed in a great gasp and sat up in a flash of motion. Casting about as though confused and staunching the flow of blood from wounds made when no blood flowed. That done the handsomely slender man lit a torch on its holder with a flick of his fingers and a word. Looking through the aged parchments sitting neatly on its surface. Other than the paper there was only a dust covered robes perched on a chair back. All the other gear he remembered planning to cache was missing. No matter, he swatted the worst of the dust from the robes and donned them before searching his memory for something he remembered planning. Hidden under a floorstone the tables legs had rested upon was his component pouch. Relieved at least a little the man spoke words of power and vanished from the bare not-tomb.
He reappeared in a place he knew well, his kitchen by the big round table. And he saw the one thing he'd truly worried about all along. She was just as he remembered her, reddish blond hair, that smile. At the soft rush of his form filling the previously empty space she turned. Rushing to him across the brick flooring and throwing herself into his arms with joy. Just then he caught motion from the corner of his eye. A shape and color that seemed to fill his mind and call to things he didn't know existed in him. The bright full moon emerged from the clouds in the kitchen window, and the beast awoke.