I agree with Rhen, looks like a drastic difference in mesh density between the cylinder and sphere. You’re also making the resolution way higher than you need to for any sort of render. Even for a hyper realistic, high resolution end goal, you should use subdivision surface modifier with a “manageable resolution” if not a “low resolution,” also low resolution is relative and basically when people say “low resolution” with subdivision they’re just saying you have a manageable cage for the subdivision modifier, not that you’re making a low resolution model ultimately.
Is there a specific reason you’re trying to do this operation via joining a sphere to a cylinder?
I would recommend:
Shift + A, add a sphere
On the Add UV Sphere box at the bottom left, click to expand, adjust segments/rings as needed. Consider leaving it around 32 segments as opposed to something like 128 which I would consider too high for starting off a sphere mesh in most cases,
Tab to enter edit mode.
Press 1 numpad to go to front view, toggle 5 until top left says front ortho
or use backslash \a
Press A or alt+A to deselect if you’ve accidentally selected anything.
B to box select bottom half
X for shortcut to delete, delete vertices.
B to box select some top nub, E to extrude:
G to translate, Z to constrain that move to Z axis–if you didn’t move it up while extruding (right click to cancel movement while extruding):
Of the highlighted verts, scale with S, constraint to Z axis, select 0 to make flat if you want a flat bottle, or just scale it down to flatten a little:
Expand selection with Ctrl and Numpad +, then S to Scale, Shift Z to scale on all axes except Z:
(not that you have to do that, just an idea)
Alt Rightclick, or Alt leftclick to select edge loop (latter is for plebeians with more typical default settings):
E to extrude, right click to cancel movement. G to translate, Z to move down. Or you could move it down while extruding.
Select all, S to scale shift z to scale on all axes except Z axis to make it more of a narrow tube (middle in below pic) or scale the entire thing down and then alt click select the bottom ring and translate it down to make it more tubular without “dehemisphering” the top of the bottle.
Significantly more geometry used than needed. To demonstrate how powerful subdivision is:
Subd with the right of the two bottles having a mean crease (shortcut: shift + E, drag mouse to right and click to finalize) on the two edge loops near top.