Material of my mixing bowl

Melamine is quite a soft material and wears quickly. Not only would metal and hard plastic mixing utensils wear it down, abrasive ingredients like sugar, oats and so on would take little bits off the bowl's surface. Over time, it is common to have pits and grooves carved into the bowl. These small indentations are hard to clean properly and could trap colours. In warmer and more humid climates, they are great habitats for molds, living off the trapped micro-scraps. Both or either could be the source of the dark spots. Melamine should not be microwaved or used with boiling water. At high temperatures (pasteurization temp is too high from memory), decomposition happens with toxic releases.

Glass (clear borosilicate or Pyrex), glazed pottery and stainless steel (in that order) are preferable in my view for abrasion resistance and non-reactive properties. I generally avoid using stainless with any wet alkaline ingredients. Also, you cannot microwave a metal bowl. I would however go for stainless if I need to heat or chill the contents rapidly.

Hm. I can think of two reasons for the dark spots.

1) Simple discoloration. Most plastic products, including melamine, suffer from this to some degree.

2) Abrasion of a layer of paint, although the only melamine bowls with additional painting I've ever seen were pet food bowls.

The only reason for the irregular shape I can think of is thermal deformation, maybe the bowl sat on a surface that wasn't cooled down yet.

Considering the state of science, it is very difficult to make a sound recommendation regarding the best material. How various popular materials affect the human body is under extensive investigation and what might be safe today might be a bad choice tomorrow. The material of choice for most kitchen products is stainless steel, which is unfortunately also the most expensive.