(1) What (real-world) physical problems are usually modeled by Ito process (stochastic differential equation, SDE)?
Here are some links as mentioned here What practical applications do SDEs and SPDEs have?
Generally, the main difference with pdes is adding a degenerate process as a potential term that simulates random forcing from the environment. In statistics-ling it represents the sum total of all the confound variables that we can't identify but still affect the system.
Especially, (2) what is the physical meaning of the Brownian motion term? Is it a measurement error? or an accumulative mechanical error? or what?
As mentioned here Why is Brownian Motion so Big in the Theory of Stochastic Differential Equations? too,
any phenomenon where you have a lot of iid interactions eg. gas particles clashing, you get Gaussian universality ie. you have central limit theorem showing up for the various statistics involved. And since people care about the variation in time of those statistics, we also get random walks and in turn Brownian motion.
The most common occurrence of Brownian motion is in simulating random forcing.
So for example, as observed by Robert Brown and later Einstein in modelling the motion of pollen particles follows Brownian motion law as being moved by individual water molecules (these are the iid hits i.e. each hit by water molecule is assumed to be an iid occurence).
But it is also indeed a good model for error. Why? Because again there are many confounding variables that are assumed to act in an iid-manner. For example, the average height often follows Gaussian law (Bell curve) because there are so many different influences each of which adding/subtracting inches (eg. genes, diet, exercise etc).