those jars are designed to be vacuum sealing, keep the lids slightly loose so the inner lid can move around, then vacuum out the air, once you open the valve the inner lid with automatically seal itself. you'll find much better results this way as the seal is near perfect.
I’m a microbiologist in training and I think I know why the vacuum was disturbed. The answer is not likely that the seals broke or air got in, but more so the microbes and fungus living on the food created their own atmosphere. Many microbial decomposers are anaerobic which means they don’t need oxygen and occasionally don’t even need air to survive. Where you left the unsterile food exposed to unsterile objects, decomposers contaminated the samples and went to work regardless of air pressure. The lack of pressure may have disturbed some of them, but by the looks of it, mostly cells with cell walls survived because the cell wall helps to regulate the cells size and shape, resisting the vacuum chamber. As they broke down the saccharides (sugars) in the food, they created oxygen and carbon dioxide. Also, there could be traces of other gases depending such as nitrogen depending on what parts the microbes and fungus decomposed and what types of metabolisms they use to respire. Water could also be created through respiration which is why the bread may have been even more moist than it was to begin with.
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