In Nanotechnology: As all we know that bulk properties of materials vary significantly at nano scales. For eg, bulk gold is a good conductor whereas nano gold is an insulator!
In Rheology: The elastic modulus of water is zero as it is a liquid. But when we probe at molecular level with light frequency, it turns out to be 109 Pascals!
In Light Scattering: According to the light scattering theory (optical range), a homogeneous medium, take for example pure water should not scatter light as there is no refractive index change inside the medium. But, in reality it scatters! Why? At the microscopic scale due to the thermal energy, density fluctuations arise and this lead to change in refractive index locally and hence scatters light!
In electricity and magnetism: The net current produced in any conductor is zero in the absence of external bias. But when you look into the microscopic level, even the free electrons produce a finite current of Pico or Femto amperes! In the same logic, one can think of finite magnetic moment in micro scales even in diamagnetic and paramagnetic materials.
In Solid mechanics: When a tensile stress is applied to a material (assume in the shape of a cylinder) along its length, it experiences a linear strain. It is macroscopically correct. But when you look into microscopic scales it is not so. We know that all metals and alloys are polycrystals i.e. having different grains with different orientations. Therefore, when you apply a tensile stress, it is tensile only to the grains whose crystal orientation perpendicular to applied stress and the remaining grains will experience shear strain in addition to tensile strain!
Emergence of Statistical Thermodynamics: Thermodynamics deals in such a way that any system is characterized by single macro state and basically it is a macroscopic study when the number of particles is large (ideally no of particles, N is infinite). The new branch of physics, Statistical Thermodynamics has emerged from Thermodynamics as the micro states become dominant in deciding the bulk properties ( N--> finite) of a system/ensemble.
In Molecular Spectroscopy: At first look, each electronic energy level of a molecule appears to be single. But it is not so. Each electronic level consists of a number of vibratrional levels which in turn each vibratrional level contains number of rotational levels. Infact the electronic transition between two electronic states (macro) is controlled by the vibratrional states (micro) present in them (Franck Condon principle).
In Dynamic Equilibrium: In reversible reactions (Chemistry), there exists an equilibrium called dynamic equilibrium in which the reaction rate of the reactants (to products) and products (to reactants) are equal. So, as a bulk, it is in equilibrium but in the micro level, still the reaction continues! Examples include dissociation of weak acids (eg acetic acid), formation of hydrogen iodide etc
Still many examples can be given. I will stop here and look into subjects other than science.
In Economics: The entire economics is divided into macro and microeconomics! Macroeconomics deals with collection of individual firms/systems or in simple it will treat anything in bulk and give single value for a state or country etc. On the otherhand, microeconomics deals with the individual systems and firms. Many times both give contradictory results. The best example is the financial collapse of United States in 2008 whose economy was basically driven by macroeconomic models.
In Sociology: Sociology is the best example for the micro and macro differences. Any sociological system like country, religion, ethnicity, community etc varies very drastically in any macro and micro scales (time, geography etc). India is the best example in all the cases.
In Marxism: Marxism is a successful macro model. There is no doubt in it. Because of this reason it fails in micro scales. For example, according to Marxism (Historical Materialism), any mode of social structure develops its own culture. For eg, Feudalism develops its own culture, morality etc and when it transforms to Capitalism, things associated with Feudalism will also be transformed. But in reality, it is not so. When we look deep into the micro scales, still much feudal, tribal culture dominates! Examples include Castism in India, Influence of Confusianism in China, Korea & Japan, Influence of Religious beliefs in important issues (Recently, Dr. Savita Halappanavar issue) Racism in European & American countries etc which are basically rooted from Feudalism and Tribalism.
In Linguistics: Any linguistic region characterized by a single language appears to be monolingual. This may be correct in writing. But when comes to spoken language, microscopic analysis tells the language differs in different regions and even it differs based on communities!
Mob Violence: Any mob violence is characterized by the behaviors of group (macro) not based on individuals (micro). Infact the individuals of the mob may be quite good people. But the moment the mob forms on certain common emotional issues, it turns out to be violent. I think this can be applicable to any group which aligned on certain common issues.
In Indian Philosophy: In Sankhya philosophy, the entire universe is considered into two entities, ‘Purusa’and ‘prakriti’ (a macromodel). On the otherhand Vaishesika philosophy which considers the entire universe is composed of atoms (micro model). Interestingly, philosophy of Yoga parallels with Sankhya whereas philosophy of Indian logic (Nyaya philosophy) parallels with Vaisheshika.