Why doesn't the wage level on my LCA match my H1B lottery wage level?
These two wage levels are controlled by two different agencies, and represent two different things. Many applicants will notice that their LCA wage level is lower than their lottery wage level.
Every H1B position is assigned an SOC code. An SOC code is a generic job description like "Software Developer," "Financial Analyst," or "Marketing Manager." Every SOC code has four different wage levels that correspond with normal wages for entry-level versions of the job (level 1), all the way up to senior versions of the job (level 4). The exact salary at each wage level will depend on the physical location of the worker.
As an example, here are the four wage levels for the Software Developer SOC code in San Francisco:

Lottery Wage Level
Determining your lottery wage level is simple. You pull up the wage level chart that applies to you, and find where your offered salary fits in. A San Francisco Software Developer making $150k would be categorized as wage level 1 for lottery purposes. The same person making $190k would be wage level 3. (For details about how your wage level impacts your chances in the lottery, please see our article on the new weighted H1B lottery system.)
LCA Wage Level
The LCA is a form filed and certified by the Department of Labor, and later submitted along with your full H1B application if you are selected in the lottery. The DOL wage level system is more complicated than USCIS's lottery wage level system. DOL's version is designed to tell the company the minimum salary it is required to pay an H1B worker so as not to depress wages for US workers in similar positions.
The DOL uses the SOC code and physical worksite location to pull up the same four-level chart pictured above. From there, however, the methodology changes. The DOL will ask things like: What level of education is required for competence in the particular role offered by the company? How many years of experience are required? Are there any unusually unique skills required? And how does all of this compare to what is required for a typical version of this job?
The more complicated and senior the position is, the higher the wage level, and that wage level sets the floor of what the company is legally required to pay.
Why the LCA Wage Level May be Lower than the Lottery Wage Level
Because the DOL's wage level sets the legal minimum that an H1B worker can be paid, the DOL wage level can never be higher than the lottery wage level. There are no rules, however, preventing a company from paying an employee significantly more than is legally required.
A recent CS graduate with very little experience may impress a potential employer in their interview and be offered a salary much higher than wage level 1. If she if offered a starting salary of $190k, she will be assigned wage level 3 for lottery purposes. Because she has only a bachelor's and little experience, however, DOL will still consider her job to be wage level 1, regardless of her high salary. In this case, her lottery application will indicate wage level 3, but the LCA filed with her full H1B application will indicate wage level 1.