How can dm_db_index_usage_stats show 0 for user_seeks and user scans but a large number for user_lookups?

The user_lookups are lookups in to the index. The original scan or seek will have been on another non covering index.

For example

CREATE TABLE T
(
X INT IDENTITY PRIMARY KEY,
Y INT CONSTRAINT UQ UNIQUE NONCLUSTERED,
Z CHAR(8000) NULL
)

INSERT INTO T(Y)
SELECT DISTINCT number 
FROM master..spt_values

GO

DECLARE @Z INT
SELECT @Z = Z
FROM T 
WHERE Y = 1

GO 1000

Gives the following plan

SELECT index_id, user_seeks,user_scans, user_lookups
FROM sys.dm_db_index_usage_stats
WHERE object_id = object_id('T')
ORDER BY index_id

Shows 1,000 seeks on the NCI and 1,000 lookups on the CI.

index_id    user_seeks           user_scans           user_lookups
----------- -------------------- -------------------- --------------------
1           0                    0                    1000
2           1000                 0                    0

BTW: Just in case you were not aware the user_lookups shown here refers to the number of times a plan was executed containing the lookup operator not the number of lookups that actually occurred. e.g. Both of the following increment the counter by 1 despite performing 0 and 2,161 lookups in reality

SELECT  Z
FROM T 
WHERE Y = -999

SELECT Z
FROM T WITH (FORCESEEK)
WHERE Y >= 0