Objects that are smelly and are semi-disgusting are not considered muktza.

Chapter 310 Section 2

Food is never muktza, even if you put it away to sell. However, if you set aside fruits not to be eaten [like grapes set aside to become raisins], and they become inedible [while they were drying], then they are muktza.

Chapter 310 Section 3

If an object was not muktza at the beginning of Shabbos, even though it became muktza in the middle of the day, if the issue that caused it to be muktza no longer exists, it is not muktza the rest of Shabbos.

If an object is muktza bain hashemashos [twilight], it is muktza for the whole Shabbos.