There were worrying signs of trouble
Although Poles offered only sporadic resistance, and Soviet leadership characterized operation as "military walk" and not a real war, number of deficiencies were noted. Stalin himself acknowledged that in his speech to Soviet leadership in spring of 1940. In his own words, Polish campaign spoiled Red Army and strengthened spirit of complacency, but following major flaws were revealed :
Slow and inefficient mobilization of both the reservists and material means like trucks and other mechanization, horses etc .. Mobilization centers were too far from frontline units, civilian authorities did not cooperate with military authorities and sometimes did not understand their role in military effort. As a result, both reservists and material were critically delayed and usually arrived in their units with 7-8 days of delay, sometimes when the operation was already over.
Rear area services (logistic) of the Red Army failed completely. They were not prepared for the operation, were often immobile, could not supply frontline units with fuel, food, forage and ammo, sometimes didn't even have enough uniforms to issue to the soldiers. It was estimated (a bit prophetically) that in case of a clash with stronger opponent than Poles (with strong air force and armored-mechanized forces) rear will suffer significant losses.
Communications inside Red Army were also deemed insufficient. Lack of radio, poor quality of mobile radio sets that did exist, and immobility of larger and more powerful radio stations. Insufficient communication with air force, especially concerning cooperation with ground troops, insufficient command and control of tank corps which proved to be too cumbersome as an organization (thus decision to disband them on the eve of Barbarossa) . It was also noted that armies and fronts (army groups) often did not have an idea where theretheir units were, and this painful flaw would latter reveal itself in full light during German invasion.
Finally it must be noted that losses in the campaign were not small. Especially worrying was loss of around 20 aircraft and around 150 (120 by some accounts) armored vehicles (tanks or armored cars). According to some accounts most of these were not lost in action, but due to various mechanical breakdowns or crew incompetency. It was noted by Soviet authorities that in many units there was simply not enough trained personnel to handle modern and more complex equipment .
Overall, Red Army was enormous system with impressive number of soldiers, tanks, guns and aircraft. On paper it was strongest army in the world at that time. But internal organization of this complex organism was severely lacking. Communist were obsessed with huge numbers, but seriously lacked knowledge about maintenance, logistic and command & control. Although Polish campaign was short it did show many potential flaws that latter materialized in Winter War and even more so when Germans invaded in 1941.