Walt is starting to fear for the life of himself, his family and Jesse - he doesn't want to do anything to risk upsetting Gus, including removing excess meth from a batch.
Consider the conversation you're referring to:
WALT Better over than under.
JESSE Over by a pound and a half? I thought you were all, like, “precise.”
Whatever. I’ll just save it out till next week.
WALT We ship it as-is.
are we, running a charity?! C’mon man, we’re gonna take it out!
Leave it. One batch, one ship. Stop complicating things.
Why are you purposely giving him free meth?! These
bitches are bleeding us enough already!
WALT You are paid
extraordinarily well, why can’t you just appreciate that...
Now, before we analyse this, remember that later in the episode Walt goes to visit Gus and this (long) conversation takes place:
GUS How is your brother-in-law?
WALT He’ll live.
GUS Good. I’m glad.
Walter, you seem troubled. How can I help you?
I asked to see you in order to... clear the air. There are, uh, some
issues that could cause a-a misunderstanding between us, and I think
it’s in our best interests to just lay cards on the table.
GUS Well, that’s the best way
to do business.
WALT My brother-in-law, moments before he was
attacked. Someone called to warn him. I believe that same person was
protecting me. Those two men, the assassins... I believe I was their
prime target. But that somehow, they were steered away from me to my
brother-in-law. Because of this intervention, I am alive. And
yet I think that this person was playing a much deeper game. He
made that phone call because he wanted a shoot-out, not a silent
assassination. In one stroke, he bloodied both sides, set the American
and Mexican governments against the cartel and cut off the supply of
methamphetamine to the Southwest. If this man had his own source of
product -- on this side of the border -- he would have the market to
himself. The rewards would be... enormous. We’re both adults. I
can’t pretend I don’t know that person is you. I want there to be
no confusion. I know I owe you my life. And more than that, I respect
the strategy. In your position, I would have done the same.
One issue which troubles me. I don’t know what happens when our three month
GUS What would you like to happen?
WALT You know why I
do this. I want security for my family.
GUS Then you
have it. Three million for three
months, that was our agreement. Extended annually, twelve million a
year. Call it fifteen. Open-ended. Would that be agreeable?
Now, just two episodes earlier in One Minute, Hank was shot by the Cousins. Walt is very well aware of this and is increasingly becoming aware of the severity of his position. He only wanted to get into the business to make money for his family and get out. Now, he's realising that may not be possible. He's very much trapped at the will of Gus. He has to do what he wants and that thought is scaring him. He feels helpless and powerless. Whilst Jesse notices the extra meth, Walt has no interest in doing anything that could risk angering or upsetting Gus, regardless of the financial implications.
Later, he does indeed go to visit Gus and very cautiously lays out what he knows - that Gus was the reason Hank was shot and that it was done to protect Walt. Walt even goes as far as to say he agrees with this strategy, before nervously inquiring about what happens to him after the contract ends. He's told his situation can be "open-ended".
Consider the title of this episode - Kafkaesque. This was a word coined by Franz Kafka, which refers to a relateable, yet surreal situation, with a sense of impending danger.
That is exactly where Walt finds himself now. On the one hand, he is only alive because Gus intervened and redirected the assassins to Hank - both saving Walt and increasing his dominant grasp on the meth business. On the other hand, he's fully aware that he is totally at the whim of Gus and could either be released at the end of his contract, killed, or forced to work on. All of these realisations are becoming apparent to him.
His solution? Continue his work as normal and do nothing to upset or anger Gus. Instead, he wants to a model employee, as he really is starting to fear for his own life, for Jesse's life and for his family's life.